SMD solder failure due to probing? How to solve it?
I suspect your idea is correct. 

First, it shouldn't be too hard to fix the damage - take an Xacto knife and bend the solder "lips" upward, then touch up with a very fine iron.

Second, invest in some needle-tip probes. These will make good contact with less force, and will also leave smaller divots.

Finally, whoever did the debugging should be shown your pictures, or even better, shown the board. If you don't know which person did it, show them all.