So I have this huge interior cell nearly as big as cells can get without glitching, and I have about 89 NPCs or actors in it. Also the NPCs are not all packed together, they are spread out, and obstacles are between them, so I don't think it's all of them reacting to the player. What could be the cause of this? Also all of the NPCs have custom IDs so no mod conflicts. Is that just too many NPCs for Skyrim to handle or is it some other problem?

If anyone has any answers for this mystery I'd be very thankful. Edit: Closing and reloading Skyrim fixed this problem for some reason.

Sorry, never mind.

Sometimes NPCs fall through the geometry and end up in oblivion. With that many NPCs, the chances of that happening goes way up. If you suspect that, you can use the console commands:

prid {Ref ID: XXYYYYYY}

moveto.player

Where Ref ID is the reference ID of the NPC in the editor render window (in his/her home cell where you placed them). Don't forget that the first two digits of the ref ID are the mod index of your mod. This would move the NPC to the player from where ever they are, if they are still alive.