I am making a town overhaul, recently I cleaned it then worked on it again. When I go into the game to test it it seems that almost every NPC added by the mod si doubled. Meaning that there are two of the EXACT same NPC in town, I have experienced this before but it has never been this bad. How can I fix this, I use esp cleaner for all my projects. I tried resting actors but that did not work. How can I fix this?

You likely need to update/repair your save file with Wrye Mash.
You should do this every time you alter your load order in any way, which does include updating esps you're working on.

I've never really used wry mash but I guess I'm gonna have to.

Solved. Close at OP's request.