[Slick]

Ok, some definitions:

sector: 1 square in the system

system: the screen on the left. All planets in the system have the same name followed by a roman numeral, and letter for moons. If you click on one system on the lower right hand galaxy map, you then have that system shown in the large left hand side pane.

Next, it is in the FAQ:

4.3.9 When a facility has "only one per system/planet effective", it refers to the ability of the facility, not to that specific facility. Eg: A System Robotoid Factory III and a System Mineral Scanner III do not stack, because they use the same ability (to affect minerals production). (Imperator Fyron)

Next, the message you get is because you already have a facility with that system ability, not necessarily the same facility, and also, not necessarily the same effectiveness.

Slick.