“Bubbles” in slumping
It is difficult to be certain, as you do not give the temperatures or rates of advance for your slumping, nor the shapes you are slumping, but would put a small bet on too high a temperature or too long a slump. If either of these occur, the glass can begin to move within the mould. As there is no where for the glass at the bottom to go, it rises. So I call these uprisings. They are not bubbles in the usual sense.
Using a pre-programmed schedule gives these kind of results. The programmers have no idea of the mould or glass you are working with, so they put in some middle of the range idea for a slumping programme. Secondly, even if you are doing your own programming, you need to observe at intervals for a short time each to see what your glass is doing. You will learn that thicker and thinner glass in the same mould behaves differently. You will learn that simple curves are different from complex curves, sharp curves are more difficult than smooth ones, that small diameter moulds work differently than large diameter moulds. So with those number of variables you cannot expect a pre programmed schedule to work all the time.
An observation: you would (rather I would) never bake a cake without checking on it near the time I expect it to be done. Why we expect to walk away from heating glass and still expect to get perfect results still eludes me.
Refiring: Sometimes it is possible, but you need to make it flat first. If it won’t flatten easily, then yes, your project is doomed to be started again from scratch. This time peek in the kiln during the 50C prior to the expected slump temperature. I bet you will find the slump is completed considerably before that part of the ramp is done. So be sure you know how to stop the ramp and proceed to the next before you start slumping.