Are these load doors (ie leading from one cell to another cell)? Or animated doors (ie in the same cell leading from room to room?
If they are load doors make sure your NPCs have intelligence over 30, any lower and they cannot use load doors.
If they are in the same cell it's possible that the radius of their AI pack is large enough that they don't need to go through that door to detect reaching their marker. Try setting the travel location radius to 0 and see if that helps.
On either door type you might check ownership. If the door or location the door leads to belong to anorher owner or owned by a faction your NPCs are not part of they won't use the doors.