I have seen the same issue sometimes, on the galaxy map : fleets are selected but they don't want to target the planet.
Also, sometimes the first click does not register, I need to click 2 - 3 times before I hear the "beep" feedback (my mouse buttons are OK).
It also manifests in a more visible way which does not affect gameplay at all, but I don't know, they might share the same origin :
-put the mouse pointer over a junction between 2 planets --> the junction gets larger
-click (left or right button) down --> sometimes the junction gets small again, sometimes not (i.e. the click is not registered)
-release click --> the junction gets large again
-quickly double click and hold second click --> the junction gets small everytime on the second click
-click 5 times per second --> the junction seems to react to every click
windows 7/64bits, windowed 2540x1320, current game performance was 100%
Damn, now I can't hate my coworkers anymore when they hijack my release threads with bug reports