In the construction set, I made an NPC to test a glitch in a plugin. After playing the game and finding it was attacking me, I deleted it and deselected the plugin, but it's still there when I played the game. However, when I checked the construction set, it said that the NPC Mal Mibishanit (the NPC I had) was not in Balmora. I checked the data files in the window that pops up before the game starts, and it said that the plugin was not selected, and that Mal Mibishanit was not in it. How can I fix this problem, and what is the cause of it?

Note: Yes, I did save.

Interacting with the NPC created a reference of him in your save file, so it is being remembered.
Update/repair your save file with Wrye Mash to remove him.

Installing the Code Patch also prevents most of these glitches from switching mods mid-game.