Has anyone else had this problem?
Sure. It's really common. As I've gone along, I've learned to use a new bit every time I do this and also use a proper rebar cutting bit for going through rebar. This has helped me get the holes perfect. If they are even a little bit oversized, the bolts won't bite as consistently.
The last four 3/4” x 6” bolts tightened up but there is only about 3” embedded in the concrete.
Are these the ones that came with the lift? If your slab is thicker than 4" and you drilled all the way through the slab, you could pound these all the way through and go with a longer bolt to help you grab deeper in the hole. Usually the bottom of the hole is going to be tighter. (The bit shank hasn't had the time to ream it out wider.)
JeepJohn62's suggestion about the tap-and-turn has also worked for me some times.
there is only about 3” embedded in the concrete. The other bolts are embedded almost all the way.
This may not be the case. These bolts stretch as we torque them. If you look at all the threads that moved up over the nut as you torqued them, that will give you an idea of the stretch. Subtract the amount from your deeper bolts from your shallower bolts, and that will give you the true delta that you are off.
Your situation may be OK as-is. If you call Bend-Pak, they may ask you for those measurements and the number of threads that you can see and should be able to tell you if you are deep enough.
If Bend-Pak confirms you are good, you are better off like this than trying to do something "inventive". Epoxy bolts are not an optimal solution and can be dangerously inadequate if not installed perfectly. (If epoxy or some other material is needed, Bend-Pak will instruct you on the type and proper material to use.) Wedge anchors are the most reliable anchor for this application, which is why they ship with the lift.