Flags have been used for millennia as ways to quickly communicate important information, and the red flag in particular has long indicated danger or warning in everything from naval warfare to racing. Whether this is owing to the color’s high visibility, its connotation of blood and fire, or something else is anyone’s guess, but it has been adopted globally as an urgent indicator that one who sees it should stop or pay attention.
As color is not reliably available in user interfaces, only the most important meaning of a symbol with many potential colors survives. So it is the meaning of the red flag that immediately comes to mind when one sees the shape.
“Flagging” content in digital contexts has a long history, with the idea that one is waving a flag at or from the content in question. Usually the flag means a form of “needs attention,” whether that’s a violation of rules, a bug, or just something that needs a look. But generally the message is that something is not right, and as such the flag has developed into a more rigid symbol in this context, a far cry from the flexibility of semaphore.
The flag depicted may be rectangular or pennant, vertical or angled, but the meaning is the same regardless of this or other details.