Theres a bug in Vault.
Do it this way. (you may have to drop and start again)
1. After you exit the station, go towards the ally ship..
2. WAIT for the fighters to get their first shot at you.
3. Use phasers or default torperdo and kill the fighters one by one. Nuking them in one shot seems to trigger the bug.
4. Kill all fighters
5. Kill heavy plasma torpedos.
6. The status to change to "Stop reman ship"
7. Now go guns ablazing on the warbird.
8. The warbird should now go ka-boom..
This worked for me after it got bugged twice , both times had I one-shotted the fighters with torpedos. used phasers the third time and took them out one-by-one and things went smooth. This is an old bug... Cant belive its still there