Usually a body shop will only do what they have to. They will make it look good enough to get it out the door. I know a painter here in my home town that HATES running a buffer and he has perfected spraying clear to the point that he doesn't have to very often. If there are no holograms on the side they fixed I would be surprised if they would have touched the other side unless it was rough enough that they needed to try to match the new shiny side by shining up the other side. On the other hand, it sounds like you have spent a little time with this vehicle so I think you would have noticed them before so there is only one place they could have come from. I also think that going back to the shop to have it fixed is not the best idea. As stated above, if they did that in the first place that is what you will get as a "fix" also.
If you need to set your mind at ease about it you could call or stop in and ask if they did buff it. They will probably tell you how they did it at no charge and "doesn't it look great?" type of BS. At least you would know you need to find a new shop for next time.
Just remember not to seal or wax that new paint until it has fully cured out. the shop should have given you a time frame (usually around 60-90 days).