how to repair holes left by expanding anchor bolts in concrete
This is a pet peeve of mine, I use lag shields and anchors for this kind of thing because those expansion bolts are such a pain if you want to move things, and eventually you move everything.  

I see you got the big-hammer solution, people love giving that advice.  ("Just pound it in!  BFH (big hammer) solves everything! What could possibly go wrong?") I'd be worried what that's doing to the concrete, and if you miss, you're going to mess up your floor.  

First thing to try:  loosen the nut and put a prybar under there, or a claw hammer, whatever, and see if it pulls out.  Sometimes if the hole is overdrilled and / or the concrete isn't that hard, they are easier than you'd think to pull out.  

At the risk of giving a big-hammer solution, if you whack the nut horizontally in all directions, regular sized hammer is adequate, it may crumble the concrete enough that the thing pulls out with a claw hammer or prybar.   

Another one that might work:  tighten the nut with a wrench until something gives.  Of course you'll need something sturdy that won't spin between the nut and the floor.  The bench's hold-down bracket may work.  If it snaps off it will probably snap off well below the surface, epoxy it and forget it ever happened.    

I normally just cut them off flush with a hacksaw, but there are other ways to go ... same ideas as in this answer.   

I wouldn't worry about the next person;  it's going to be very visible there's something there, and people always need to be cognizant they may hit metal when drilling in concrete.  

You could drill around it with a core bit and snap off a core that would just lift out, but that's way way more trouble than I'd go to unless you happen to have a core drill and a small bit lying around.  

EDIT:  I thought of one other thing.  You could get a hammer drill and a bit a little bigger than the bolt, and drill down right next to it.  That will weaken it's hold enough that you can get it out with a little persuasion.  Then you can fill the hole with the epoxy.  A hammer drill and bit that size is much easier to get a hold of than a core drill.