I'm confused which part of this is so off-putting.
Joe is always the one in every standup saying the thing he's working isn't done yet because he's wrestling "one last tough bug." As a manager, you wonder if the technical problems are really that tough or if Joe is just struggling. Let's look at the commit history... yeah, something is off here, Joe has 1/10th the commits of his peers and they really don't seem more complex in any way, but look rather trivial. Time to talk to Joe and look at these commits together and see what's going on.
So troubling that you can't propose it cleanly: if you've already defined that "they really don't seem more complex in any way, but look rather trivial", why would you need to count? (another troubling sign is going for the order of magnitude assessments, and another minor point: you've mistakenly replaced volume of code with # of commits)
Joe is always the one in every standup saying the thing he's working isn't done yet because he's wrestling "one last tough bug." As a manager, you wonder if the technical problems are really that tough or if Joe is just struggling. Let's look at the commit history... yeah, something is off here, Joe has 1/10th the commits of his peers and they really don't seem more complex in any way, but look rather trivial. Time to talk to Joe and look at these commits together and see what's going on.
Is that really such a troubling proposition?