So, I collected the anti-cube in the clock stage while falling.
The fall killed me, but I did collect the cube, the music played, and there was a close up on Gomez's dead body. I didn't keep track of how much cubes I've had, so I don't know if it counted. I teleported back to one of the hubs (the clock stage has a teleport up top), and the anti-cube was floating in the air in that stage. I collected it... again, and it did count that time for sure. The problem is, I still have a question mark on the clock stage, even though I collected the anti-cube there, and I feel I did all there is to do there.
So... uhh... am I still able to get "get all the collectibles" achievement?