What happens is that a dupe stands idle next to the Oil Well, doing nothing, but the Well and the Dupe seem to be reserved for "emptying". At the end of the cycle, the dupe leaves, the Well unemptied. Next cycle, it usually works. Save & reload makes it work.
One special condition: I only feed the Well 500g/s of Water, so it starts/stops all the time. Hence this looks like a race-condition somewhere in there.
In the attaches save, with backpressure set to 1%, I see this about 2 times in 10 emptying events, hence it is not that rare. A few minutes at most should make it happen.
Seems to be random. Not really rare though, I saw it in 2 of 10 emptying events in an experiment with the attached save. Run the save for a few minutes and wait for it.