Sometimes the orbs are not in the immediate area of the puzzle. You need to go find them.
I have the exact same problem as OP, and there is no orb to be found. We both did exactly as the game intends, we squeezed through the gap, pulled the box from up top, turned the gear to melt the goo and the orb that is behind the goo normally is simply not there. I even make backup saves and used one from before I entered the area, and there was no orb there then either.
I’m having the same problem. I even looked up a video of how to do the puzzle. The orb just isn’t there. Either it never spawned at all, or I accidentally pulled it at some point while interacting with the box. Either way there is absolutely no way to progress at this point
