Thats not really a glitch, it's just what happens when stuff gets trapped in doors. Try it with grenades on castle1.
Having said that, not having the flag respawn sounds like a problem, I've never experienced that myself.
Dag
p.s. Don't have secret rooms or passageways in your map, they always suck.
edit:
I just tried it, and this is a bit weird. The message 'ERROR: Red flag not senthome after timelimit' appears in the console, but I think this is because the flag is already returned (at least it was when i tested it on KungFu).
What game mode is your map?