"Red flag" has become a slang term in schools (at least where I Live) meaning "watch out, this kid might go Columbine!". Someone must have seen it on some TV show or heard it on the intercom or something, and it just caught on. It implies, in jest, that this is a potential problem (in the sense that jonlasser was talking about) and the offender ought to be referred to the authorities. You say it when someone makes an offhand, joking threat of violence . For example:

"I'm getting a C in biology."
"Haha, you're an idiot."
"I'll kick your ass."
"Uh oh, red flag!"

I guess it makes one realize just how common a device this in in conversation, at least among hormonally driven teenagers. It's also a somewhat embittered shot at a system that now thinks everyone in this country is liable to fly off the handle just because they threatened to kick someone's ass. Lighten up, America.