The Mw chapel windows were accidentally added with the wrong ID so they ended up overwriting the pc ones This has since been corrected (https://www.tamriel-rebuilt.org/asset/pc-chapel-interior-window-restoration) but it does mean that the windows used in the Grand Chapel of Akatosh need to be swapped out to account for the new IDs
During quest for Old Ebonheart Fighters Guild with healing Foenus Locutius, when force feeding him the cure he says: "What kind of vile liquid is this? I am being forced_from_this mortal's body!"
In the topic "Tel Oren", Nethan Marys (TR_m1_T_Nethan_Maryis, Mistress Faruna's mouth in Port Telvannis) has slightly outdated instructions. Namely, it still refers to Tel Oren being on the tip of a peninsula, as it was in the original Telvannis. However, since this line was written, EoE has now moved Tel Oren onto an archipelago.
In fact all the directions should be tested for correctness as a whole, as EoE rework may have rendered them faulty in other ways.
The quest "Noises Off" (TR_m1_PT_NoisesOff) in Port Telvannis starts as soon as you hear the latest rumor. I believe this is not up to TR standard, the quest list should only get populated once you actively click on a quest topic (or somesuch).
Seems to be a running theme in the Armun Ashlands, NPCs in shan-ahhe generally have mediocore skills/equipment for their level. They're all using exclusively auto-calculated stats. Worst example is "TR_m4_Vraggo the Wrangl" whose only weapon is a spear with a skill of 11 in spear. Same general story for the others.
TR_m2_tel_guard2 has a low light armor skill compared to the other Telvanni guards. You probably wouldn't notice during normal gameplay, but with mods that increase fUnarmoredBase2 they won't wear most of their armor because they have a higher armor stat without it.
For the same reason, Staron in "Tel Mothrivra, The Glass Goblet" won't wear his shield.
The NPCs in piransulit are all level 15-18, so mid-high level by base morrowind standards which caps out at around 20. But they have stats and gear of low-level enemies. The armun kagoutis outside are more dangerous than them. All of them have auto calc'd stats.
The cave appears related to TR_m7_HH_Sathis4. Based on the NPC scripts they're also related to a bounty quest of some kind. The hostile NPCs within all have auto-calc'd stats. Some specific examples below
TR_m4_O_Vanu: She has the quest related Ebony axe that is very valuable and does a lot of damage, but she has an axe skill of 36.
TR_m4_O_Rathys: He has an Iron great mace and a blunt weapon skill of 14
TR_m4_O_Nalmen: He uses an iron mace and a mix of light and heavy armor. His blunt weapon skill is 36, light armor is 11