This has been happening a lot recently, and I can't figure out for the life of me, why, but I've been entering dungeons and found parts of them missing. I, for sure, have encountered this in Nightcaller Temple (The floor at the entrance was missing), Dead Man's Respite, and Ioverth's Liar, or whatever it's called. I don't encounter this glitch in any normal interiors or in any exteriors. Just dungeons. I'd post a screenshot, but I apparently can't.

I'm currently running 1.6, and this is my load order:


? 00 Skyrim.esm
? 01 Update.esm
? 02 Populated Cities NPCListMaster.esm
? 03 SkyMoMod.esm
? 04 WARZONES - Civil Unrest.esm
? 05 JSwords.esm
? 06 WinterholdDestruction.esm
? 07 RaceCompatibility.esm
? 08 Quest_SeaOfGhosts.esp
? 09 Unofficial Skyrim Patch.esp [Version 1.02]
? 0A SoS - The Wilds.esp [Version 1.0.1]
? 0B SkyrimURWL.esp
? 0C Economics of Skyrim.esp
? 0D 3DNPC.esp
? 0E ENG_All_In_One_v1.2.esp
? 0F Birds.esp
? 10 BooksBooksBooks.esp
? 11 Catsofskyrim.esp
? 12 Cowardly horses.esp
? 13 Dwemer Spectres.esp
? ++ HorseMarker.esp
? 14 SkyMoMod_lists.esp
? 15 Skyrim Scaling Stopper - Misc Edits.esp
? ++ Skyrim Scaling Stopper - Vanilla Dragon Scaling Patch.esp
? 16 Tytanis.esp
? 17 Berserk Black Swordsman Armor - No Arm.esp [Version 1.0]
? 18 1nivWICCloaks.esp
? ++ Craftable Staffs.esp
? 19 Dwemer Scouter.esp
? 1A Field Mage Outfit.esp
? 1B GeraltJacket.esp
? 1C HedgeKnight.esp
? 1D Insanity's Chrysamere.esp [Version 1.0]
? 1E Insanity's Empire Longswords.esp [Version 1.0]
? 1F Insanity's Sorrow.esp [Version 1.2]
? 20 JSwordsDistributionBalancePlugin.esp
? 21 King's Slayer Armor.esp
? 22 LFArmors.esp
? 23 loners_sword.esp
? 24 Iorveth.esp
? 25 NightsWatchArmor.esp
? ++ Non-playable Armor.esp
? 26 Omegared99-WeaponSets.esp
? 27 Saskia.esp
? 28 Shields_of_the_northern_kingdoms.esp
? 29 TH3WICK3D1-GeraltSeltkirkArmor.esp
? 2A ThalmorStandalone.esp
? 2B TrissStandalone.esp
? 2C W2_HelmetPack-2.esp
? 2D W2_HelmetPack.esp
? 2E Quest_AndTheRealmsOfDaedra.esp
? 2F BreezehomeLibrary.esp
? 30 ExpandedWinterholdRuins.esp
? 31 Radiance.esp
? 32 RiverWood Redux.esp
? 33 WARZONES - Civil Unrest.esp
? 34 WARZONES - Optional Performance Pack.esp
? 35 Whiterun Ferns.esp
? 36 whiterunMarket.esp
? 37 WhiterunFortified.esp
? 38 WhiterunREVISION.esp
? 39 DynamicMerchants.esp
? 3A FasterHorses_Sprint_x1_5.esp
? 3B HeavyImperialLegion.esp
? 3C Hypothermia.esp
? ++ Ish's Weighted Gold.esp
? 3D killable_children_1_01.esp
? ++ Light Blades Armor.esp
? 3E VariedGuards.esp
? 3F riverwood gates.esp
? 40 Populated Cities.esp
? ++ Sprint6.esp
? 41 Battle_Mage_v1_1.esp
? 42 MidasSkyrim.esp
? 43 DeadlySpellImpacts.esp
? 44 mpn.esp
? 45 Skyrim Scaling Stopper.esp
? 46 TrueYield.esp
? 47 LovelyHairstyles.esp
? 48 TheEyesofBeauty.esp
? 49 Better Followers - Beauty P.esp
? 4A Better Followers - P.esp
? 4B BDO.esp
? 4C Alternate Start - Live Another Life.esp [Version 2.0]
? 4D Height Adjusted Skyrim with True Giants.esp
? ++ First Person Messages.esp
? 4E Bashed Patch, Skyrim.esp
? 4F cremation.esp
? 50 Omegared99-ArcherArmor.esp
? 51 Omegared99-Stark.esp
? 52 Cloaks PC Only.esp

Yes, I know, I've got a /lot/ of mods.