I haven't got BFME2 installed right now so i can't see for sure, but i'm guessing EA has deleted the scripts for the multiplayer version of the map. The waypoints shouldn't affect the AI's building system, as that is done through the AI libraries, and not individual maps.
I'm guessing those waypoints are leftover from the campaign missions, where the scripts tell the AI to build a specific building in a specific spot.
thank you