There's no problem in bridging both ports, in fact it is needed for transparent layer 2 connectivity.
Problem is if both networks are already layer 2 - connected, as you would be creating another link, and thus, a network loop. RouterOS (R)STP detects this in the bridge, and disables one port to break the loop.
Which networks are you linking? Are both linked by other means already??
Have you by chance used backups (not .rsc exports) to "clone" one radio config into the other??