Seams to me someone should fix these. (lol). I've confirmed that this has been here since vanilla and hasn't been addressed in the thousands of mods I use... Well I've got something to say to you.
IT. IS. TIME!
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Changelogs
Version 1.1
Fixed hole in Kodlak's bedroom.
This mod attempts to address visual issues for objects in Jorrvaskr.
At this time, it creates a custom mesh that works with the existing wall to cover the hole. It also corrects the hole in the door mesh.
I am awaiting permission for ELFX regarding some pieces which appear to have been modified in ways that appear to cause minor seams in the whiterun dungeon tileset.
Skyrim Landscape and Water Fixes (SLaWF) - WizKid implemented his own fix as part of version 7.2. You can use this mod alongside that one without issue. I am.