I had only two oil on my map and thought it was the same old bug, however at one point I noticed 'Build Oil Well' in the production queue of one of my cities on the bottom of the map.
I had full vision on every square in that territory, and there was no oil marker. When I tried to build the well, though, there was a lit hex, and it allowed it, and at that point the oil marker appeared.
Don't know how much of the missing resource bug is a visual bug for markers, and how much is actual missing resources, but figured this was worth mentioning.
I faced the same issue with Uranium - actually I already had 2 sources in the same city, so I thought it is a bug that UI still offer to build a mine after it already been build. After reading this topic I checked my game and found invisible source in a water (on south-east edge of the Cahokia)
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