Yesterday’s daf (50) was talking about leaving uncovered water out and how we’re concerned that a snake could come and drink from the water, thus injecting some of its venom into the water. If you were to want to drink the water, the gemara offers the following solution: filter it, even on Shabbos. The question is asked, but if you filter the water on Shabbos, isn’t that borer? You are specifically trying to separate the bad (the venom) from the good (the water)?
The reason we allow people to filter water is because we’re not sure that there is something bad in the first place. It is only there as a precaution. You might not be filtering out anything bad. In this day and age where filters are commonly found in people’s homes, it is not necessary to disable the filters just for Shabbos because there might not necessarily be bugs or whatnot in the water.