You should have noticed already that NavyField is not the fastest responding game. For instance, if you turn your ship, it doesn't do it right away, but waits a few miliseconds before doing so. Similarly, the guns do not fire right when you press *spacebar*, but has a few miliseconds delay.
THEREFORE, to properly drop the bombs, you need to either (A)Spam the "." key OR (B)Hold the "." key before your bombers approach the manual target that you have set.