Well actually it's what happens with this type of navigation when any robot crawls. A browser keeps track of the current path and figures that the ./ means current directory while ../ is the parent directory (i.e. up one level). But if you use ../ and the base href does not indicate correctly what the full path is with then the robot is lost.
I'd have to see the page to figure out what's going on. But in general it's best to avoid such relative urls that leave room for ambiguities.