Fighters remove all markers on a 1 to 1 basis, and never has been any more than that.
So, examples:
- 1 Fighter removes 1 Fighter
- 1 Fighter removes 1 Bomber
- 1 Fighter removes 1 Assault Boat
- 1 Fighter removes 1 Torpedo Salvo
Let's take your example:
1 Fighter moves into contact with 2 Mantas. It attacks the first marker. The Manta rolls a D6 for its resilience and it comes up a 4. The Fighter is removed from the table and the Mantas stay in place without harm.
Alternatively, should the Manta have failed its resilient save, it would be removed too, leaving a single Manta marker in the way.
What you were getting mixed up is the effect that a Fighter has on ship turrets.
For what rules you should use, read this thread:
LINK.