It is impossible to work on a water damaged phone without leaving some traces behind. You have to heat the shields to several hundred degrees in order to remove them. The black stickers on them will shrivel and crack and are easily scratched.
Removing and replacing IC's requires flux and it tends to get all over the board. A good micro-solderer has all the right tools to do this quickly and effectively. They will also have a high quality ultrasonic cleaner to clean the board afterwards.
The videos we see online are just the successes...very rarely will we see the no-fix failures.
I can't speak to the quality of the repair shop you worked with but expecting a pristine logic board back is a little unrealistic, not to mention that water damaged devices are the most difficult to repair. Talk to the shop and have them explain what they did. Visit their workbench or watch videos yourself to see what's involved.