I was going back to my first map to look it over, which is generated from a master tile set. Up until yesterday I had no issues with which tiles could be crossed by the player or not but all of a sudden I'm encountering a big problem. Normally, I've had the first and second layer able to create barrier, such as the water tile forming rivers, undulations making short hills, etc. For whatever reason, now only the third layer, (topmost before the event layer) seems to retain these properties. Essentially, I can cross almost anything unhindered now, but some tiles still block me, with no clear reason as to why.
tl;dr Unknown why I can walk across tiles that normally would stop me. Seems to be layer related, but inconsistent.