My suggestion:
1) if the fleet has only fighters that came from ships, don't score any vp for destroying the fighters.
2) if the fleet has only fighters that came from independant flights, score VP for destroying a whole wing's worth of fighters, regardless if they came from the same wing or not (avoids book-keeping) Example: if you have 6 starfuries (two wings) and destroy 4 of them, score VP for 1 patrol choice. This should not boil over to craft of a different type, even if they come in the same numbers. Example: you have 6 starfuries and 3 thunderbolts (3 patrol choices). You destroy 4 starfuries and 2 thunderbolts, you get credit for 1 patrol choice killed.
3) if the fleet has a mix of craft (some from ships and some from independant flights) then treat as 2) until the same number and types of flights have been destroyed as were purchased as independant flights.
example: if you have 10 starfuries (two wings and those from an Omega destroyer) you get VP for a patrol choice for destroying 3 starfuries, no matter which ones they are, up to a maximum of 6. More than that and they're assumed to be from the Omega.
Chernobyl