As in they let you go "under" them and then not let you back out or you can't pass through them at all preventing you from getting into certain places like Feron's house entirely? If there are specific sticking points on that map I can do some tweaks but I'll need to know where they are.
After taking a look this morning, as I wasn't around my computer when I got notified about your post, I figured out what happened even if it shouldn't have broken the way that it did. It should be fixed in the newest version and I scrubbed through the other tilesets and found a few other situations that needed fixing as well.