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See screenshots. In version 2.0.11 on the planet Fulgora, I suddenly have a mixture of liquids and can only get it fixed if I remove the electromagnetic plant and put it back in. When I was turning it, it happened to me once that liquids could be swapped around. Even though I had removed every pipe, after putting in a new pipe, crude oil came out again, even though the output is different. One factor seems to be when electromagnetic plants are right next to each other. If there is a chemical factory in between, everything works.

Thanks for the report. This is actually expected behavior. The EM plant has an internal fluid buffer that is separate from the fluid segment, which is where the filter is applied. This is necessary in order to facilitate the mechanism that allows input-starved machines to consume fluid evenly.

I have some plans for how to make this behavior more intuitive that I will be implementing in the future. For now, simply flush the heavy oil via the pipe GUI.