I assume you are talking about other cities you can't see due to not having units near them?
You probably weren't paying attention for a few turns and missed a prophet attack. AI sometimes hold onto them and buy several and do mass conversions. Celts and Ethiopia come to mind as the usual culprits. I've seen 3-4 prophets at a time come at my lands and I have to block them with units because they have no attrition. You can know for sure by mousing over the city. If it has zero presence from other religions or just 1 then it was probably prophets because they erase even the minor religions from the city. Natural conversions that take time usually have several religions present.
Probably there was 1 or 2 prophets and they converted a number of cities. Missionaries can convert especially no-religion cities. Maybe Inca built Hagia Sophia or Leaning Tower so he had a spare prophet?
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