My ancestors on my mother's side of the family have been members of the same denomination since the Reformation. I was floored when I read the obituary for two of my great-great-grandparents and it said the funeral was at the local Presbyterian church.
The small town they were in only had two churches. Neither was of the desired denomination. The Presbyterian church was "closest," so that was it.
It is possible that necessity caused your ancestor to attend (and leave records at) a church other than the one you think he always attended?