There was an indie game that had 4D puzzles (as in actual 3D + time), and the person/team behind the game developed a framework and map editor to work with those properly... I cannot recall the name, but it looked awesomely complex!
Was the game Miegakure [0]? It has the same author as this paper/post, and pretty much seems to be the premiere 4D game. The parent link says that the research shown here was developed for Miegakure, so it might be the game you're thinking of. [0] - https://miegakure.com/
Wish people wouldn't call "game with time manipulation mechanics" "4d" though.
I do remember there was a game which was like, an rts, but with time manipulation bits.
Ah, but that didn't really feature 3d movement, so probably not what they are thinking of?
I also remember a 4d spaceship shooter game..