The timing is all over the place for "normal" days. There have even been days where no trending subs were posted at all or they were posted more than once in a single day.

There's also the matter of the cut-off time for trending. It doesn't run from midnight to midnight. The cutoff seems to be early enough that it's entirely possible that the entire kerfuffle started after the cut-off point and some of the fallout could appear on the list tomorrow.

There's also the matter of nothing ever having been said to indicate that these are the "most" trending subs. People seem to think that but they have no reason too, especially considering the times that there have been multiple trends posted in the same day with the lists being entirely different. Even if /r/coontown is the most trending sub in the history of trending subs, that's no guarantee that it will make the list even without manually manipulation.

Which isn't to say that the list hasn't been manipulated. There's absolutely no doubt that the list is handled manually, considering one of the mods admitted to accidentally pushing the list through twice the first time /r/circlejerk trended, causing it to be knocked off the trending list. (They caused themselves to trend again the next day, however, without incident.)

This is all to say that it's possible that the list was manually edited to avoid any of the controversial subs. It's also entirely possible that the list is completely legit. The important thing is that it's not really a topic worthy of discussion, thus my 271 word comment about the matter.