As far as mobs are concerned the world is a flat plane, so whenever you raise or lower the ground it means their pathing no longer "see" your constructions as being in their way, and they just walk right through them like they don't exist.

Not sure if the new AI will change this or not.

This is basically the same issue as other glitches with creatures going through walls so I'll close this specific report.

All these issues will be resolved with the upcoming AI changes (many which are on the current Test Server - but I haven't patched a final path finding system yet).

Thanks!