Yes, when a faster person says, "good job," to me I am pissed that they are faster. It feels condescending. Good job at what? Being slower than them? They don't know anything about me.
I realize quite well that this is in my head. But, I don't think some realize how this can make someone feel, when you are trying as hard as you can and can't go any faster, for whatever reason.
Most of the time, I don't want to be going faster than I am at any given moment. But, I would appreciate, a "hello", or "nice day" comment more than "good job." I know when I pass someone going slower than me, I just say, "good morning", or whatever.