I recently ran into a problem where, upon returning to Moon Grotto, it would be impossible to make it past the second laser, as there seems to be a bug that resets the lever in the area, or something to that effect. I looked on discussions, and sure enough, plenty of other people are having this problem, and not being able to get the last few collectables. It looks like there was a script for the original game that enabled debug mode, but it doesn't work for Definitive Edition. However, I managed to find someone suggesting an alternative.

Onto the solution itself: (I highly recommend backing up your save file before attempting all this) With the game closed, create an empty text file in C:\Temp called "moonDebugPC.txt" without the quotes. Then load your game, press Ctrl+8 to enable debug mode, enable Invincibility, close the debug menu with Ctrl+8 again, then walk through the problem laser at your leisure.
Then, this is important, go into the debug menu and disable invincibility, create a soul link to save, then quit the game to desktop. Just for good measure then delete the empty text file, reload the game, then collect the missing item and continue playing. If all goes well achievements should still be active.

I'd credit whoever had the easy method of enabling debug mode, but I honestly can't remember where I found it.
Also thanks to the user on the discussions page for this game suggesting I put this as a guide as well, to improve visibility of this fix.
Hope this helps with your 100% completion!