EDIT: Disregard this, it was indeed my mouse malfunctioning. Sorry.
This happens to me rather often in PF on XUbuntu Linux (at least once every minute). It doesn't happen in other games I play or in my desktop so I don't think it's a problem with my mouse. How exactly it happens:
1) I do a single click on my ship, and yet several ships are group-selected.
2) I click on "NEXT" in dialogue and I skip TWO dialogues forward.
Does the game run normally otherwise? Is it running normal speed or does it seem sluggish?
It runs perfectly normal, I have very powerful PC. The CPU usage is negligible (certainly under 10%).