Its not so much the heights you have to worry about its more bone structure. Generally you want to breed the finest boned stallion you can find to your mares. Never breed a heavy boned stallion to a fine boned mare.
Some of the problems are as said above. A big one is many miniatures can't break the bag so they suffocate if no on is there to break it open for them. This is why if at all possible you have to be there for the birth.
The other problem is if a foal is not aligned correctly you don't have near as much room to get your arm in there and fix it. But it can be done.
Over the years we have only had 1 that we could not correct ourselves and it was a stillborn. Those are difficult because the foal is dead before labor starts so it does not move into the birth canal