Summary: Bartenura gives his answer; I give my own, that maybe it is not out of order, and if it is, it is a logical order.
Post: In parashat Tazria, we encounter the following pesukim and Rashis:
My focus in this post is on the Rashis in pasuk 14, but I give the Rashis on pasuk 12 for context, for a reason that will become apparent shortly.
On pasuk 14, it seems like the explanations are out of order. First, d"h וביום הראות בו בשר חי, which would seem to be on the entire phrase, and we consider it more closely, specifically on the latter part, בשר חי; and then, d"h וביום, interpreting the first word of the verse.
R' Ovadia mi-Bartenura asks this question, and offers an answer:
"It is difficult, why does he twist about the Scriptures, that he explains basar chai before he explains uvyom, which precedes it in the verse? There is to suggest that because, if we had explained that the verse comes to explain the laws of מחיה, 'live flesh', I would have said that this which is written וּבְיוֹם comes to inform us that even by מחיה, which is an extremely strong sign, which is readily apparent to the eyes, even so, we can only see it during the day, but now that it comes to teach us a different law, why is וּבְיוֹם needed? Therefore it explains a different explanation thusly: there is a day that you see, etc."
I don't find this explanation so convincing, in each reach into the underlying assumptions of the derashot, and plausible alternate derashot. I would instead offer three other, more straightforward (IMHO), suggestions.
First, perhaps the Rashis are not really out of order. Refer to this Munich manuscript of Rashi I keep referring to, from 1233, we find that in fact it has the Rashis ordered by the order of the pasuk. Thus:
I marked up this text will a few red underlines, for each dibbur hamatchil. The first is מראשו, from pasuk 12. Then, לכל מראה עיני הכהן, from pasuk 12. Then, on pasuk 14, וביום הראות בו בשר חי. But this one is followed with מה תלמוד לומר, ללמד יש יום שאתה רואה בו! And finally, without the leading word uveyom, d"h הֵרָאוֹת בּוֹ בָּשָׂר חַי. Thus, in this manuscript, the two explanations are reversed.
However, I would caution that there are quite a number of textual insertions in this manuscript of Rashi, often pulled from midrashim. So perhaps this scribe felt free, as well, to "correct" the order of Rashi. If so, lectio difficilior applies. And it applies even more once we see the third explanation I offer.
A second, straightforward explanation is that if we examine the content of Rashi's two comments, we see that the first comment explains the main thrust of the pasuk. Don't we know מחיה already, asks Rashi? Therefore, this entire pasuk has a different general meaning, which is then to fit into the surrounding context of the other laws of metzora. Once we establish that, we can focus on a specific tangential detail which is a midrash halacha derived from one of the words of the pasuk.
The third, even more straightforward explanation comes from checking out Rashi's sources, which we can get from Mekorei Rashi. The earlier Rashi is drawn from Sifra. The second part of the later Rashi, regarding the regel, is also drawn from the Sifra. And the order in the Sifra is the same as we find it in Rashi:
So why blame Rashi? It seems to me that he is basically learning through the parsha with the Sifra and other Rabbinic texts, and selecting out salient midrashim as he progresses. Indeed, he cites quite a lot from Sifra on these parshiyot in Vayikra, as I have noted in other posts. So why shouldn't he cite it in the very same order it appears in the Sifra? He should.
A separate question may be why the Sifra puts it out of order like this. And perhaps Bartenura's answer applies, or perhaps not. This is similar to a question of why Mishnayot are ordered in the way they are ordered. But at the least, we have a lot more raw material to work with. Perhaps it is based on features of the various disputes / discussions between these named Tannaim, in the first, between Rabbi Meir and Rabbi Yossi, and in the second, between Rabbi Yehuda and Rabbi. Thus, the first between colleagues, and the second, between teacher and student of the next generation. Or some other feature relating to the content. But we have more material from which to determine an answer, plus we can distance ourselves from the very question and assert that it is not part of the job of a supercommentator of Rashi, but rather a specific type of analysis of midrash halacha.