That was not caused by AV, then. AV does not place new animals or anything like that. ASIS does, somewhat, with Increased Spawns.
You know, the problem is probably that people are not starting fresh games. However, that issue is mostly Bethesda, not any of the patchers such as AV or ASIS. Also, starting clean is required for actual testing of anything or there is no way to tell what is truly causing a problem, if a problem happens.
I use Skytest with AV and have since I started using both of them, and no problems at all (again, aside from things I know such as trying to change midgame and getting skating animals, but that's Bethesda, not the patchers).
By the way, there is a bug tracker for AV. For example, it is known that AV cannot handle Extended Colors, probably because of the thousands of variations from Extended Colors and AV does similar functions (plus Java limitations). However, any mod that is not desired to be included can be unchecked prior to running the patcher (similar to how Bashed Patch looks for active mods, not inactive mods). Some people do this for ASIS for mods such as dragon buffs, although ASIS also has a file that can be configured for records to exclude. I find it much simpler to just uncheck a mod I don't want to include, at least for now.