Big thanks for this comment. I am having the same red boxes trouble for quite a while now. I have checked many times if there is any overlapping mesh problems like you explained but i only have simple other mods installed like new armor or a weapon which i believe it doesnt have anything to do with my problem since when i try installing new mod huge building have red boxes on them and only door or some mod related npc have red boxes on them. My guesses mine is its core/vanilla skyrim issue (I have Skyrim Special Edition btw) or pc specs or the mods which seems unlikely to me because i tried many different mods with different outcomes . So can you guys direct me to any kind of solution ?