Yeah, some mods leave data in your save file that stays behind when you uninstall the mod, causing problems down the road. Mods that have scripts that run in the background are particularly problematic, unless the mod author includes a method for stopping the script from running. A lot of mods do that through the MCM. DynDoLOD is one such mod that I have safely uninstalled from a save by carefully following Sheson's instructions. I am not sure whether this type of procedure will be available on console, since the MCM needs SkyUI and SKSE, and I don't know of another way to do it without at least being able to enter a console command.
Even mods without any scripts can add data to your save that cannot be changed. For example, the global variables that set room rental, cart ride price and horse prices, as well as bandit bounty quest reward amount are baked into the save at the moment of character creation and can never be properly changed after that.
Some mods, like my mods Immersive Ingestibles and Superior Standing Stones can be safely uninstalled but only if you follow certain procedures to make sure all the affects on your character are reverted to vanilla effects before uninstalling (can be done in game without needing the console or the MCM).
The best advice is to never uninstall a mod mid game, but you can do it with some mods if you follow the author's instructions.