[2020] Water pollution even with a filter

The filter does not filter all pollution. You might also have air pollution around that will cause ground pollution as well.

No, that has no effect. There always will be a slight pollution left, but that shouldn't have any real consequences if you're not around with twenty of them. In most cases this happens it's actually caused by the air pollution dropping down in biomes with medium or higher rain simulation, as typically workbenches that cause air pollution are near filters.