If you fire a torpedo at a ship which then cloaks, the torpedo will still accurately track and hit the ship despite you properly losing target lock (after the ship has fully cloaked itself). Ideally, if the ship has fully cloaked before the torpedo hits, the torpedo should also lose target lock and count as a miss.

On a related note, when a targeted ship cloaks, you lose target lock immediately, as opposed to what would make sense - you should lose target lock when the target has fully cloaked, not before. The same behavior should apply in reverse to a decloaking ship - it should show up as targetable immediately upon decloaking, even with its shields down (this is canon, there's always a risk with cloaking and decloaking in combat, I fail to understand why it's any different here).

The reason is because the Klingon captain needs time to say 'to be or not to be' before the torpedo hits. If he can't get it out in time, the torpedo tracks...

I think this will probably get tweaked up to the standard you said as the game gets tightened up.

the torp should be able to guess your flight path by your speed and direction of your last position. push comes to shove they should make it a 30% chance it will hit

Also, the 'to be or not to be' thing.

Torpedoes tracking after cloak is initiated is intended, and part of the cloak balancing. I'd rather have a period where the shields are down but everything stays locked, and then drop tracking for any projectile weapons that haven't hit by the time cloak is total, but this way kinda works.

I wonder if its also a function of the way attacks/hits are calculated. Does the game check when the weapon is 'fired' or when its projectile/beam/etc 'hits'? Its kinda the same thing on why when you duck around hard cover on ground maps sometimes you still get hit.

If it checks when the weapon is triggered/fired, I don't see a way to prevent it, other than cloaking before someone actually fires at you.

I agree with this - simply having a torpedo continue to track a cloaked target to "balance it" just takes away from the experience. If you implemented the logic behind shields when cloaking and decloaking, then there's your balance.