John, In retrospect that is an obvious answer. I only witnessed close up a peeling several years ago in the early 90's. Immensely obnoxious noise and the cutter head would create ripples exactly as you describe. The machine I saw was a cutter head on a articulated mechanical arm that was robotically controlled by a joystick. There was a vacuum setup but in spite of that the operators view was limited. I remember thinking that more damage than good could easily be done in moments in the hands of an unskilled operator, which is true with any power tool. And "OJT" training means some less than perfect work. The cutter was carbide and could take off gelcoat and part of the first layer of mat in one pass. Like I said the noise was very very bad and after watching once I stayed as far as possible from any such work when in the yard. Fortunately I'm retired and was when I watched the peeling and so there is no job requirement to be present. Hopefully newer better machines are doing this work but the one I saw in the early 1990s would easily produce such ripples.
Aside from cosmetic after effects (the ripples, poor fairing afterwords) did they replace any laminations removed with epoxy or vinylester layup or simply overcoat and call it good? If they can give you a date when this was done and if there has been no further blistering then the job was successful from that aspect save that it was less than beautiful. If you wanted to verify replacement of removed layup you might pull a thru hull and get a visual x-section of what was replaced.