I encountered this issue both in my big modlist and then tested it in a new game with only TR installed, so I can be sure it's not an issue at my end.

Doing the first Imperial Legion quest in Old Ebonheart (Merchant DIspute) I was sent to the Barristers Guild to find about the rights given Vols Valdri (one of the merchants).

Issue 1
The fist NPC in  the basement of the guild (Reynant Alciente)
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has the "merchant dispute" dialogue option and says "I don't deal with trade law. Ask upstairs." But this dialogue results in an journal entry "A member of the Guild of Barristers told me that all assigments of land must be approved by the Duke." In my opinion this journal entry should not happen with this NPC.
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I also suggest to give the duke a dialogue option for "merchant dispute" at this point. Maybe he can give some interesting informations or options. At the time he has none.

Issue 2
After confronting the merchant with the fact that he faked his paper he gives in and the dialogue shots down with a black screen (time transition I guees, mabe something changes in the cell?). After that both merchants still sand in place and react with strange dialogues. Vols Valdri acts like he was victorious in the dispute, even if he was not, and the [Arrest] options lead to a fistfight witch should not be as the player is an Imperial Legionnaire and the market is full of guards.
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Only after reentering the cell both merchants react as they should.