In Santorini Central, when removing the Quick cycling filter, there are two identical options to install it on the rover and back into the station. Some sort of verbage differentiating them from one another would help solve this. It does separately track your completions so if you keep track it should be obvious after the first time. This is if you have the water recycler in the rover already, with there being a 2nd recycler already there.
Are you playing the free (v0.4.5 in the bottom left of the main menu) or paid (v0.5.0) version? The paid version should have this fixed. The free version will catch up with content in about a month, though if I get time I may look into a "mid-step" version which has all the bug fixes and UI improvements.