Should shingles have bubbles in a new roof?
Bubbles in a roof like this are NOT normal. They indicate a problem underneath. Is it serious? Possibly. It will probably decrease the life of the roof.

The shingles will have been nailed down, so this is not a case of the shingles simply pulling loose. Especially if the roof is soft there, it seems this must be a case of the plywood underneath having gotten wet and as it dried out, then warping and bubbling up underneath. The plywood should have been replaced where there were problems.

Edit: After seeing the interior picture, it looks like there was some water contact there at some time. Is it still happening, or is this old, perhaps when you had the hail damage? I find it useful to use a moisture detector - Wagner Moisture meters. It is something I have for woodturning purposes, but it is useful to resolve problems like this. You may be able to rent one, since it hardly seems worth buying one for one use though.

If there is still moisture there, it is possible that water is still getting in, that the roofer made a mistake somewhere. Water can be insidious that way, getting in the tiniest of cracks.