[Arkangel]

The primary objective in one of my missions requires you to force destroyers out of the area and destroy fighters left behind. It registers the cruisers leaving but doesn't register the fighters being destroyed when they are. I've got a SEXP to trigger it when each of the individual wings is destroyed (all in one event) so i don't get why it doesn't work.... 
 
Fighters have several waves each and come from separate destroyers if that gives light to my predicament. And i don't think all the waves are deployed before they jump out usually

[karajorma]

That's your problem. If all the fighters in the waves aren't destroyed then the SEXP will never turn true. You have to be a little more creative with the SEXPs you use than a simple is-destroyed-delay.

[TrashMan]

Problem is that if the destroyer from which 5 waves of enemy fighters are lunching is destroyed BEFORE the 5th wave laucnhes, it will never come. Ergo, it will never be destroyed.

Now, since I haven't bumped into this problem myself (given that I use smaller wave numbers when launching from destroyers) I'm not sure how well  I can advise you. But let's try a few methods:

1. You can try destroyed-or-departed. I'm not sure if the game will treat the wings that never arrived as departed.

2. Have more different wings instead of more waves.

[Arkangel]

Okay, sorted that out and the mission now registers when the wings are destroyed as i chained a message to the event. However the objective still doesn't recognize it 

The objective is basically [is-event-described above-true] and [is-event where ships hp goes below certain levels-false]
If the false event were to become true it ends the mission so i don't understand where i'm going wrong 

[karajorma]

Look at question 2 here. I've linked you the answer. The question is the first post on that thread.

I suspect that's the cause of your problem.