Flange set too high? Wrong DIA Pipe?

I recently hired a plumber to repipe my house with PVC. When he finished, I didn't notice immediately that the two upstairs toilets are, respectively, 1/2" and 7/8" above the finished floor. THe gaps were filled with a horrible looking putty that has crumbled. The plumbers won't come back out, so I pulled the two toilets to see what the problem was and found that the toilet horns are sitting on the flange that the wax ring would normally bottom out on. The horn is 3.65" OD and the pipe below the hole is 3". I assume that the horn is supposed fit into the pipe. How do I fix this?

Horn? do you mean toilet flange? can you take and post a pic?

A flange is supposed to sit flat on (and be bolted to) the top of the finished floor level with only the thickness of the flange above finished floor level for the wax ring to seal properly.
If the flange is too high, as both of yours seem to be, the toilet will rock and will never seal properly.
If those plumbers won't come back out and correctly install the flanges, I would file a complaint with your state Plumber licensing board AND the local Building Inspection Department AND have an attorney contact them.
No excuse for such shoddy work.
Good Luck!
Mike

More information

My toilets are 1940 vintage Crane Merit models with horns (the round outlet that extends from the base 1/2" lower than the perimeter of the toilet) that have an outside diameter of 3.65". The plumbers installed a flange that tapers down to a rim that has a 3.0" inside diameter. It is this lower rim that the toilet rests on. I'm now told that the horns on older toilets were larger than on current models and that if I had two new toilets they would probably fit. The flange extension fits inside the three inch closet bend. I'm told that if I cut the flange at the top and hacksaw out the remaining pieces inside the closet bend, I can find a flange that would fit around the outside of the newly re-exposed end of the closet bend. I'm not sure how it will do this and allow my 3.6" horn fit down inside of it. I'm nervous about starting to cut the flange and then finding out the correct fitting really doesn't exist. I really don't want to blast up the tile floors again. If it came to that I might prefer to replace the toilets, though it would really irritate me.

Most new toilets don't have a very deep horn...they would bottom out on the flange, and not sit flat on the floor, either.

What is the diameter of the pipe? If it is 4" you might have some options. At 4", you can get a flange that fits either inside of the pipe or the outside of the pipe. A 3" pipe can only support a flange attached on the outside keeping the inside still about 3". SO, if 4" (and it probably is), if you can get the parts of the flange out from the pipe, you'd have a 4" hole and you could get the flange attached where it is supposed to.

More information still

The three inch flanges are attached to the inside of, respectively, a 90 degree and a 45 degree three inch fitting. It looks like the plumbers machined the inside of the lower fittings or used a short length of pipe as a sleeve to attach the two pieces. At any rate, the inside diameter remains three inches. I would need an adapter that fits around the outside of the three inch pipe and would fit the inside of a four inch flange fitting.