If you are holding the flags while a team caps and gets 50 points, you should not be granted the extra points for holding the flags. This is a flaw in the game and everyone who can use simple logic knows this.
This game is based around CTF.
Simple logic:
The team with the most points wins.
If you're holding flags at the end of the match, your team gets additional points.
If your team has the most points, you win.
That's not a flaw in the game. That's just how it was designed, and it's been that way for over 10 years. This game is based on points. Capturing the flag is just one of many ways to get points. Holding flags at the end of a round or match is another way to get points. If you think the game should be changed so that you don't get points for holding flags at the end of the match, I guess we can put it up on the feature vote, but I don't think everybody will agree.