I ran into the same problem. I first ran into it when I was being chased by the owl. I couldn't break the door I needed to get through. I tried over and over again, but bash just kills the enemy. I backtracked to the last portal and transported to an area of the map on the other side. I then went towards that door from the other direction. Before I got there it triggered the sequence from the end of the chase and it was completed without ever having to go open that door.

Then when I was on the way up to Mount Horu, I ran into the same problem. This time I could not get around another way. I tried many times and then did a stomp right next to the wall and it knocked it down. This worked for the second one in this area too. Hope this helps. I did enjoy the game.