Has anyone ever encountered this game breaking issue?

[Tree]

https://youtu.be/qzVo7VAjB28  My video and it's description will show all the details. 

I asked everywhere, and nobody seems to have this problem before and I really can't find any answers. I'm not even sure this is related to mods or not, since I only have 100 mods installed and I play with these mods from the beginning of my playthrough, and now it's already more than 300 hours and all the sudden I get this bug. I didn't add, or remove any mod recently (actually I never remove mod in my entire playthrough), and my save file size is 10mb (uncompressed size is 27mb). Before I had this issue everything is totally normal, no script lag or any bug I noticed. Can anyone tell me what could possible be the cause of it? 

By the way, I got this bug in arnima, which is the world space of Beyond Reach, not sure if it's related to it though. 

I can provide my load order if it's really needed.