According to numerous sources, the samples were collected late on a Friday afternoon but not shipped until Monday, as the collecting agent reportedly believed they would be more secure at his house than sitting in a FedEx office all weekend. I personally find that argument to be somewhat suspect, but taking it at face value and assuming the integrity of the official in question, this still constitutes an unnecessary delay. Testosterone and other hormones, synthetic or otherwise, are metabolized by the body. This can be described in terms of half-life, the amount of time it takes for the body to metabolize 50% of the original amount. Half-lives vary widely between different types, and when you are testing for such substances, the amount of the dosage is also a factor in your ability to detect it. Most forms of natural testosterone have half-lives measured in minutes, but they generally aren't especially useful for unnaturally rapid muscle growth and whatever else people might take them for, partly because of their short half-life. For those attempting to abuse steroids, something with a half-life measured in hours is the way to go. It remains in your body in sufficient quantities long enough for a good workout, at least. I wasn't able to find any information concerning what specifically MLB thinks Braun was taking, but for the sake of the argument, let's say it had a half-life of no more than 8 hours, which would be exceptionally long. If the sample was shipped early Monday morning (around 8:30am, say), anything that might have been in Braun's system would have been reduced to 0.4% of the amount contained in the samples. Let's assume it took one day for the test to be conducted and the results to be turned over to league officials and whomever; 1-2 days is average if you go to your doctor to have a urinalysis, and we can only assume that this was a reasonably high priority for the lab in question. In those 24 hours, the amount left in Braun would have reduced to 0.048%, about a full order of magnitude less. I have to assume that their tests are pretty sensitive, measuring amounts in parts per million, but if Braun took a retest Tuesday morning, about the earliest he could have known about the results of the first test, it's probable that it would have been clean (as in fact his retest was), even if he had been taking something on Friday. The longer it took to conduct a retest, the less relevant the results, especially if the half-life was less than 8 hours, which is likely for anything any athlete would take.
Let's start with a summation of my argument. Regardless of whether he actually was or was not taking any banned substances, MLB cannot prove beyond all reasonable doubt that the test they conducted was legitimate, due in part to the way the samples were handled. Since it took the league at minimum three or four days to conduct the urinalysis in question, there is a high probability that whatever substances Braun might have been taking would have been metabolized enough to avoid registering as abnormal in a retest, so any efforts on Braun's part to show a clean result on subsequent tests four or five or more days later would not be particularly relevant to the results of the original test. Because the window of time had passed for the accused to have any recourse to a retest to establish or refute the validity of the original test, and because the accused was not responsible for the unnecessary delay in the processing of the original test, applying any punitive measures on that unverifiable test would be inappropriate at best.
Why would a retest be needed? Well, for one thing, if he still had elevated levels in the retest, even though they would naturally be lower than in the first one, it would be pretty strong evidence that no error in testing had been committed, and the accused wouldn't have much of a leg to stand on. (That's probably when they try to plead ignorance about what exactly they were taking.) If his retest is clean, and if it happens soon enough after the initial test, then you have to consider the possibility that one or both tests were in error. Especially when the results of the first test are as abnormal as Braun's. The most commonly reported figure was that his ratio of two forms of testosterone were above 20:1, and some reported that it was as high as 30:1 (for those who don't know, 1:1 is considered normal, and anything 4:1 or greater is what MLB and many other agencies look for as evidence of abuse). Sometimes this is a legitimate result, and it would imply that a person had either taken a massive dose, possibly an overdose, or else the test was conducted pretty soon after they had taken the substance, before much of it could work through their system. It can also indicate that something contaminated the specimen at some point, or that it had been handled improperly at some stage. If you went to your personal doctor for such a test, and those results came back, they would want to do a retest immediately to make sure that such a finding wasn't erroneous (they may want to do it five or six times if you have an indulgent insurance policy...), unless they know for a fact that you are taking something that would account for levels like that. I have seen a couple of articles suggesting that Braun's defense included a demonstration of how a clean urine sample could develop excessive hormone ratios simply by being left at room temperature long enough; apparently they contend that the hormones measured break down at different rates, which seems reasonable on the surface. I will wait for the report from the arbitrators before I assign much credence to those claims, however, as the sources are of the "friend of one of the lawyers" variety. Again, though, even if the original test was conducted completely properly on a properly handled specimen, the results were anomalous enough that under ordinary circumstances most doctors would probably recommend a second test in the interest of accuracy. But in this case, too much time had passed, as I have already said.
I have no wish to impugn the character of the agent whose job it was to collect the samples. I will take him at his word when he says they were properly handled, insofar as they were kept chilled and in a secure location. Because he waited so long to get around to sending them off, however, he eliminated Braun's best chance for exoneration by scientific means. Inadvertently done, perhaps, but in a system where you are required to prove your innocence rather than having it assumed, that still amounts to a violation of whatever civil liberties he and other players haven't given up in exchange for their lucrative careers. How could the league impose a sanction if they or their agents have mishandled the case in a way that prevents the accused of having a chance to prove his case? Indeed, how can they sanction him when they have also made their own position unsupportable by means of additional validation from retesting?
In the American legal system (and indeed in most democratic systems), a jury or arbitrator is not asked whether or not the accused is actually guilty or innocent; that's why guilty pleas proceed straight to the punishment portion of tonight's entertainment. Instead, they are asked if there is reasonable doubt about the guilt of the accused. If the evidence is not strong enough to be thoroughly convincing on its own merits, you do not punish the accused (again, in theory). The positive results from one batch of samples, taken necessarily in isolation because of the way they were handled, are anomalous enough (whether the defense was able to duplicate the results with intentional negligence or not) to merit some doubt about the validity of said results. With that doubt in mind, and with no way to eliminate it, there is simply no reasonable grounds for punishment.
As a final thought, there is quite a bit of talk about how Braun should disclose what, if anything, he was taking that might account for the presence of a synthetic hormone in his urine sample. Only by doing so can he win back the trust of the public, such arguments tend to go. I don't agree, for several reasons. First, trying to manipulate public opinion is often less easy than herding cats; more often than not, it isn't even worth the effort. There is, at this point, no evidence he can present to conclusively verify his innocence, so anyone who has concluded he is guilty cannot be countered with anything resembling proof contrary to their beliefs. Secondly, if he truly is innocent, then speculation about the contents of a urine sample that was contaminated, corrupted, or possibly not even his own is pretty pointless. Some science suggests that people in modern America are gradually entering puberty at earlier ages, possibly as a result of high levels of growth hormones found in our food that build up in our bodies and eventually reach critical mass. If Braun, or any other player, were to resort to speculations like that, the response would likely range from incredulity to befuddlement to an assumption that he is grasping at straws for an excuse. Finally, again looking at it from a legal angle, there is no burden on Braun or the defense in general to advance any alternative explanations for the results, so the only reason to do so is if it throws doubt on the official explanation (which they may actually have done, if those reports I reference earlier are correct; that story might still come out). All the defendant is required to show is that the accusers have possibly made an error in some portion of their accusation, which usually suggests that the accusers are more interested in punishment than in justice.