This has alway been the case, as far as I've experienced. I think the new patch change was to prioritise loading your party members so they don't vanish. Busy hunt marks have always been vulnerable to popping in and out of Sight - it was a major complaint when Eureka launched, too.

The beast solution I'm aware of for now is to circle around it so there are less people between you and the monster, so the system is more likely to count it within the "X closest objects" that are loaded on your screen.