im using skinny top heavy bottoms on my axe and ive just noticed that the 10 gauge e string lies right on top of the bridge before going into the saddle. its a string through body. will this cause any problems?
As long as you are not constantly breaking that string I can't see any other problems coming from that.
It really shouldn't cause any major problems, as long as it isn't holding the string at a really weird angle. In that case, it might cause you to break your E string more often. It's also another contact point to cause tuning problems, but that's probably not a real issue since it's a hardtail. You could always lower the bridge to move it out of the way of the string, but you might not want to lower your action that much, unless the saddles can be raised to compensate.
what kind of guitar is it?