“Well, where else were they supposed to appear?”
I was sent this error along with the previous question for a failed optimization. Apparently there is no answer in the internet (I quickly checked) so here it is:
Gaussian is confused about finding atomic coordinates because there is also a geom=check instruction placed in the route section, i.e., it was told to retrieve the atomic coordinates from a checkpoint and then it was given those atomic coordinates within the input so it doesn’t know what you mean and exits.
Dr. Joaquin Barroso's Blog 
hmm