Should I be concerned about this roof bubbling?
That “bubbling” (we call it blistering) is from a lack of venting. 

This is evidenced by 1) blistering in a straight line, 2) blistering around the roof jack at the 3” roof vent, 3) random blistering throughout the roof. 

1) Blistering in a straight line is an indication that heat is trying to escape and has found a gap between the roof sheathing. 

2) obviously one of the easiest places for heat to escape is around vent pipe holes in the roof. The roof sheathing AND roofing underlayment (moisture barrier) is cut for the pipe to extend up through the roof. This allows heat to escape and affect the shingles. (Notice the shingles are affected all the way around the pipe.)

3) When there are random blisters in the roof this is an indication that the nailing of the shingles in that area is not adequate/correct. Heat is escaping throughout the roof, but it is causing a blister in these locations due to a lack of nails, improper nailing pattern, etc. 

I see a ridge vent, but it’s probably not installed correctly. I’d look up in the attic and see if you can see a CONTINUOUS strip of daylight at the ridge. Often roofers will allow the moisture barrier (building paper) to lap over the opening (gap) in the roof sheathing...thus making the ridge vent useless. 

The good news is that the roof sheathing is not expanding so much that it’s heaving. That is to say, the roof sheathing was installed with adequate gaps (spacing between sheets) so that when they heat up and expand they do not bulge upwards. 

BTW, you’ve lost your guarantee from the roofing manufacturer, because they’ll see the lack of venting. 

You can verify the lack of venting by looking around the house and adding up the area of the vents. 

The Code requires 1/150th s.f. of attic vents compared to s.f. of attic, unless you have 40% - 50% of vents not more than 3’ from ridge then it’s 1/300th the s.f. of house (attic).

So, say your house is 1600 s.f. and you have ridge vents so they are in the upper part of your roof. That means you need about 1600/300 = 5.3 s.f. of venting. (I can’t see your gable ends, so you might have even more venting.)

The ridge vents are usually about 1” wide and extend the length of the ridge...say 36’. Therefore your ridge vent equals 3 s.f. (Which is within the 40% - 50% range requirement.)

So, now you need to look for soffit vents and / or roof vents. Add them up to see if you have enough venting. I’m guessing you don’t. 

Also, vents get covered up by insulation. Get up in the attic and see if you can see daylight coming in all those soffit vents around the perimeter of the house or coming in any of those roof vents. If not, you’ll have to figure out if you can unblock the vents. 

BTW, one reason you think the roof looks better now is that this picture was taken at just the right time to show all the shadows. If the sun shines directly on the roof, it will “burn” the shadows out and look great. I’d go back when the sun is lower in the sky.