It certainly sounds as if it may be mods. Whenever mods are installed, they will alter parameters of a game, which will then alter the data that is recorded when a game saves. This altered data cannot be removed. As long as the mods are compatible with the present version of a game, everything will be fine. If a game changes the way it functions, like bug fixing, new or altered mechanics, new visuals, etc., then the mod will also have to change to remain in line a game's base functionality. The mod will also need to be updated. Whether or not this affects your game depends on the mods installed, what parts of the game they alter, what parts of a game have been changed via an update, and how different mods interact with each other.
Removing mods can also be problematic, as that will remove the functionality your game is looking for (via the mod) but still leave reference data in your save state. This is where most game-breaking issues are likely to occur.
So, if you've ever used a mod that altered clothing, the way leveling works for items (including clothing), or even the look of clothing, it has likely been built in a way that conflicts with the present version of the game. Best-case scenario: the mod will be updated by the author. Worse-case scenario: the mod may need to be removed. Worst-case scenario: the update created a conflict that is not rectifiable with that mod, and it can't be removed cleanly. At that point, it may be necessary to restore a save made at a point before the offending mod was first installed, or even begin a brand new game.