Holes in basement floor
To be on the safe side:

Contact a local plumber and request that he scope the drains. 


Plumbers equipped with a snake camera can inspect the drains and tell you if there is any damage or blockage. I would highly recommend you go this route especially if you plan on finishing the basement.  Do not put a floor over these holes until you know for sure what they are. 
If you want to try and DIY, call a local hardware store that rents out these drain cameras. The draw back is that since you do not have the experience, if you find something questionable you'll need to contact a plumber anyway.
If you are really set on finishing the floors and are going to do it despite recommendations here be sure to leave some sort of access door / trap door in the event of flooding.


Good luck.