During the battle at the Goblin cave (passage on stairs leading to Caer Lem), one of the goblins desingaged from my created halfing rogue and hid behind a corner, thus breaking Line of Sight. On my turn, I chased it around the corner, but couldnt know for sure in what square it was on, so I tried to decide where to move based on the projected white lines on the movement preview. In one of the possible positions to move, the lines didnt show at all, so I believed that was a position where I would be in melee with it, so I clicked. It was actually the square the goblin was in, so we overlaped and I couldnt attack.
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Another bug was inside the Caer Lem courtyard. I used my rogue to search for traps, clear the way to the objective door. The rest of the party decided to take a shorter path upstairs using an invisible ladder on the wall and one floated on thin air upon arrival.
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Falkbeer - The Caer Lem issue is a known issue. Basically, Caer Lem gets repaired later, but the navmesh from the repair is still present (though invisible) on the first visit to Caer Lem. The developers noted that on the "known issues" on the last update.
I did have the overlapping character issue in a Wilderness location random encounter with Badlands spiders. My party was surprised while resting, and two characters were asleep. The Badlands spiders were able to crawl "on top of" my sleeping characters, though they were booted to an adjacent space when the characters were awoken by my party (in one case) and by the spider's attack (in the other case).