you just reminded me of a ctf match on orbital i had a few weeks ago. the enemy team kept spawning into our base stealing our flags like crazy. everyone on my team noticed a squad leader was in our base somewhere and everyone was trying to find him but we couldn't. then i realized that he might be under the map so i took a jetpack and went down there. i was right!! he realized that i found him and tried to kill me. i shot him with a rocket launcher.
Theres some hollowed out trees in the Cypress maps, figured it out while waiting on players to join my match.
Now if only Squad Leader gave out XP.
**bleep**. I thought everyone knew about that one by now.
Theres also one on Apoggee that you can only get to on the outcast side with a jetpack.
Edit: Err a secret room under the map I meant.