I think there's a problem with overlapping mods in TU15. It wasn't a problem in TU14 or prior to my knowledge.
For example, if you download an All in One Kits Mod, and then try to have a Kit mod for a Specific Team, the overlapping (or having two) mods for the same teams kit somehow corrupts the system and ruins it. I'm not an expert modder, just trying to troubleshoot my way through it, but I think the only problem is overlapping minikit icons. I think there's no problem with jersey/shorts/socks/
This may not be what your problem is, but it's been a problem for me since TU15, and so I've had to re-do my kit mods without adding the minikit icon in the legacy folder.