Holes in concrete basement

Have you peaked in all of the them?

The one with the blue pic looks like an electrical junction box.
Does that blue cover come off?
If they do not provide any access to anything then they surely can be covered.
BUT.....if you are not sure, draw a map with the locations so if for some strange reason you have to find them......well, you know.

It's hard to tell from the pictures, how big are they actually? Also, are they all grouped together or spread out around the room, a picture showing their location in relation to the room may be helpful.

Looks like it might be for some kind of sump pump system?

Is that some kind of printing on the diamond plate cover?

Could be prep work for a radon gas extraction system....that was never used.