As title and description suggests, I'm creating an AOD map but whenever ordering a team to follow a waypoint it moves through buildings [which is good] but also bridges [which is bad]. They have to cross quite a few bridges a few times and it looks very silly and is very annoying to have them phase through them. Any fix on this?

There is no fix for it. Moving through buildings also causes moving through bridges.

There are workarounds however:
1. Do not move through buildings (duh), use move / attack-move to waypoint instead of following a path
2. Replace the bridges with ground / ramps

Basically the only options you have.