Use more than one transport if you want to capture multiple planets. Once the troops are dropped on a planet, you can't pick them up during combat, and the only way the other planet can be captured is if they happen to be "touching" (check the squares in the mini-map). This probably will not work in strategic, as the captured planet probably won't have a "Capture Planet" strategy.
And, to prevent capturing your friend's planets, you should try establishing a TREATY.
