Hey y'all Ivan here hehe. The high score system is a little funky. Sometimes your recent score doesn't show on the main menu, sometimes it won't count the agents you killed in your last playthrough. A fix is going to be made to make sure that won't happen.

EDIT: Keep in mind that this bug won't always happen with everyone but it can *sometimes* happen to people. Be aware of this. We will make a patch if we find anything wrong.