The pirate puzzle, where you need to get them to bury your bird I found highly annoying. It's one of those puzzles that are hard for the wrong reason, I knew right away that I needed to place the talking bird in the chest but I had to figure out how the game would let me.
Having to do the stairing contest -then- the discraction didn't make any sence. Why did the pirates look away differently after the contest then just with a distraction? That puzzle was the one probelm I had.
Oh, and the thing with the fish eggs? Bad Telltale! Me no likely the red herrings! :P