One of the three letters in the Undertaker's Hut (on the wall shelf above the desk) can't be reached. Also, even after reading the diary and the other two letters found in the hut, there's no journal update, and no option to discuss the evidence with T. back in Cyseal.
It's possible to get permanently poisoned (i.e. suffer a set amount of poison damage per turn, over an apparently infinite number of turns) when attacking Pontius Pirate.
If you ignite the ooze under the Zombie Troll while he's still neutral, he'll exclaim something like "Be careful!" in English instead of in troll language; he'll then disappear.
You shouldn't be allowed to trade with Evelyn or the Graveyard Madman during your single brief conversations with them - it doesn't make sense.