So could Mary have been recorded on the 1891 census twice? I've seen people who appear in two different locations, but mostly children where there must have been some indecision about whether they would be at home that night or staying with grandma, for example.
In this case, perhaps it would be best to look into whether there was another couple called John and Mary Patterson in the same area. Can you find the birth registration (and mother's maiden name on gro.gov.uk) for their son James?
Obviously the census took place in spring and your couple didn't marry until later the same year. Have you seen the parish record or marriage certificate for Mary Ellen and John Patterson?
The transcription of the 1891 census is a bit patchy on Family Search; in case you haven't seen the images, the birthplace for the Mary who's married to John with son James was given as Newcastle. Mary the servant was said to be born in Willington.