Then you didn't do it right. If you had done it right spanning tree would have prevented loops from forming. That's what spanning tree does.
That said, you can also convert from a bridged network to a routed network.
Those are literally your only two options. Going to a routed network is going to be more work, but is also cleaner. Spanning tree will also solve the immediate issue.
It's impossible to be more specific without knowing your network inside out. If you can't do this yourself you should look at hiring a consultant. This affects your entire network, this is not something trivially solved in a forum post. If bridging loops take down your entire network then your entire network is - sorry to say - very poorly designed and needs to be looked at from the ground up.
Specific answers require specific questions. When in doubt, post the output of "/ip address print detail", "/ip route print detail", "/interface print detail", "/ip firewall export", and an accurate network diagram.