I sent two subs fro the same outpost at an enemy outpost that contained a pirate and a double agent. The enemy launched his pirate and double agent at the second ship, and somehow went straight through the first ship, even though they had colliding trajectories, and destroyed my second fleet which had my queen. There's nowhere in the rules that says a pirate will skip past ships it's not targeting, so I don't understand why this happened!

Sorry tchester. Things collide only if their going to or returning from the same pairs of destinations. Even if they look like they collide they don't.

Example

sub going from A to B
collide with sub from B to A if it reaches that sub (head on collision)
collide with sub from A to B if it reaches that sub (your sub is faster)
collide with sub that was going from B to A but is turned around back to B if it reaches it (sub was turned around by navigator or saboteur)
collide with a sub if it is the target of a pirate (a target of a pirate)
does not collide with a sub that is passing through it if any of the above is not true. (navigator who changes course to a third base)