It would make more sense that it is just a runt than being part of a late litter. At least based on all of the studies and literature that I have read. There appears to be a narrow window of time that coyotes can breed which is mid February nation wide. Possibly a week or two on either side of that. Apparently they cannot come into a second cycle outside of this timeframe, so early or late litters are highly unlikely.
Just based on information I have read and studied. I’m certainly not an authority on the subject.