I tried many things now and it's been 2 weeks but nothing seems to work. I can't find a way to overwrite the worldguard protection in faction lands.
Me asking questions gives me more information to work with. I'm guessing that you've set explosions to deny on the __global__ region. I'm not trying to judge you or anything, so I apologize if you felt that way. The reason I asked is because instead of blocking explosions with WorldGuard, I believe you can use the command /f flag warzone explosions no instead. This should block all explosions that aren't in factions. I haven't tested it myself as I run a Towny server, but give it a shot! To remove the other-explosions flag from the __global__ region just use the command /rg f __global__ other-explosions, that's it. Not specifying allow/deny will cause it to simply remove the flag if you didn't already know. In the future, if someone asks questions about your server because you made a post on the forums, there's a good chance that information will help them help you.