In the Lost in Transit quest (https://en.uesp.net/wiki/Tamriel_Rebuilt:Lost_in_Transit), you're asked to find a missing hunter from Bodrum, and the only directions you're getting is that he went "south near the border of the ashlands", which doesn't really narrow it down.
Issue: In Extrajudicial Punishment, after discovering Talen-Ei is the culprit, selecting the dialog option "a delicate matter" when speaking with Eveshi Drilor immediately turns in Talen-Ei. This creates a problem for abolitionist characters who may have started the quest out of curiosity, and who may be looking for options to close the quest lying on Talen-Ei's behalf (see: Me).
The little advice topic contains a number of duplicate lines filtered to different classes that say "There are always some real experts in certain trades. Go seek them out; who knows what you might learn?"
These lines were added to block the vanilla master trainer lines, but now that all TR NPCs are NoLore, these blockers are redundant and should be removed.
Firewatch TG, last mission where you have to return the stone of septimia, the guard at the entrance forcegreets you right at the door upon entering the museum, leaving you no chance to be caught by the other FG guard at the bottom floor, which is the only one you can convince to stay here at the lower floor, by telling him you have the college's headmaster's permission.
After that, you can normally proceed to cause a distraction by breaking the Kamal bone fragment exhibit, maybe pop an invisibilty potion/spell and sneak unhindered to the top floor.
The gap between the top floor and the stairs in the Imp_SetNord_I_Lighthouse set is impossible to walk through without tcl. I've attached a screenshot of the gap I'm referring to. Models are tr/i/tr_in_nor_lh_03.nif and tr/i/tr_in_nor_lh_04.nif
gold_dae_cursed_001 is an unused vanilla item, but TR adds it in a couple cells, Yamandikal, Sanctum and Anashbibi, inner shrine. This item caused an error for me when I tried to pick it up: "Did you add a new type of gold? It needs to be added to the TES3Container.cpp file."