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One of my turtles has dug out spot in the rocks (way bigger than their heads) about the size of it's shell. It will just sit in that spot. There is like a little tree trunk thing that is too small for them to get it, but they can put their head in it. And this turtle has made this little area right at one of the openings and will sit there, but I can't tell if he/she is puting their head in there or not. Any clues as to what this turtle could be doing?

I've seen one turtle just sit at the bottom of the tank and sleep. Don't know, maybe just resting in one of those awkward positions .

Probably just exploring. Turtles can get pretty bored in their tanks & will do funny things to pass the time!