Proper Protocol for “Complimentary Roof Inspection”

Looks like they picked it apart expecting to sell you $1,300 repair. If the shop is close I would take it back and insist they fix the damage they caused. If not, then buy a $10 tube of Dicor and a Caulking gun if needed and just fill the holes and move on. You should be inspecting and repairing cracks in the caulking at least once a year if not more.

I would ignore the bubbles unless they pop and expose the roof to water intrusion.