I had a similar problem. You may want to use a red light (like a red LED) as a flashlight and look for activity in the darkness.
When I did this I finally found the culprit. After a bit of searching on the internet I figured out I had a stone cab hiding in there. He was about 2 - 1/2 inches across.
He managed to kill off most of my clean up crew snails as well as a few fish before I figured this out. I ended up having to go to war with him and finally found him tucked way inside a hole in some live rock after practically ripping my entire aquascaping apart.
I hope you don't have to go through the same pain I did, but it sounds like you might have to...
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