They could have been more careful when installing it.
Its non appealing to the eye but i have never heard of a TPO leaking because of this. I have owner 2 with bubbles and had no issues over 11 years of ownership.
On new applications : After the underlayment is installed under new tpo roofs , it needs to be brushed clean ( or use compressed air ) to get rid of dust from sanding the edges,screwheads and seams to prevent tearing of the new tpo.
If some dust remains, the glue will not bite at that particular place, causing a bubble.
The new tpo material is cut larger than the roof top area allowing extra material to hang over the sides. As the mechanics (2) installs the edge moldings, the material needs to be stretched on each side at the same time by pulling it tight, then they screw down the moldings to hold it tight, like a drum head.
They sometimes get lazy because they rush to get these things done and out the door.