I'm sure this is a lame post but forgive me for asking.
I see this all the time in ctf maps. In map maker it shows a yellow flag. But actually in the game nothing appears. So what's the point? What does the yellow flag do?

point match mode.

Point match mode isn't really popular among the servers, but its when the person with the flag gets two points for every kill and its all vs the flag holder.

HTF also has a yellow flag

it's usually to make the map compatible with all gamemodes. i always put a yellow flag, a rambo bow, player spawns, and charlie and delta spawns on my inf maps, so it's playable in DM, RM, PM, TM, and HTF.