Some more info on body filler. Most body fillers don't typically "bubble", they "map" the repair area. What this means is that if the body filler is applied too thick and has not fully cured (this is a catalyzed product), it will continue to do so until fully cured and it will shrink under the paint which causes the repair to "map" or show where the body filler was feather-edged under the paint. The other thing that happens with body filler is that it can be affected by primer and paint. If the repair shop used regular body filler but no Metal Glaze (Fibre Glass-Evercoat product) to seal the body filler, the body filler will be affected by the solvents in the primer and paint put on top of it - another way the repair "maps".
If you have rust coming through, you will typically see raised irregular spots coming through the paint. IMO, if it has been as long as you say since it was painted, then you probably have rust coming through due to improper metal prep and/or filler left on unprepped metal too long without being sealed and it absorbed moisture and is now rusting through again.
