There are places that are cut off from the play area, such as some of the raised areas in the Dark Forest, over the river in the south east corner of the Dark Forest, in the lower sections of the sewers and outside the walls of Versistis. Some you may be able to get to by tossing a teleporter stone there, but may mot be able to move other than repeatedly using the teleporter stones.
Other than that, if it looks like your character should be able to get somewhere, try clicking and holding the left mouse button to direct them, rather than just clicking. Or move the mouse around if they could be getting caught on a tree or rock rather than walk around it.
The back room in the mage Kistandalius' shop in Ars Magicana is also impossible to enter directly, and don't even try the telporter stones; the mage will teleport you out of the room before you can do anything or pick up a teleporter stone. There is a way to distract him, though, and get a brief, one-time opportunity to loot the back room.
