So I keep getting stuck on this mission and cant find anything online. My teammates always destroy the base too early, failing the mission. It usually happens right after the base has been disabled and the shuttle leaves. I order my wingmen to do other stuff but it doesnt help.

Any ideas?

Try to identify what ship is causing this, as it doesn't need to necessarily be one of your wingmen... and you can still give some orders to non-wingmen ships. Not to all of them, tho.

The easiest way should be targeting the base and pressing A to see who is attacking the target. Once ID'ed, you just need to have that ship selected and use the keyboards shortcuts for those orders. I would try with one of these:

-Shift-E: Stop what you are doing and Evade.
-Shit-H: Go home (I think it never works with a ship that still needs to complete a mission [boarding and so], but just in case don't use it with those :D)
-Shift-W: Wait for orders.

If it's your wingmen who are destroying the station, using the "Ignore my target" order (Shift-I) while targeting the base should do the trick.

thanks, I didnt know about the "A" command. I used that to figure out who it was. I had to disable him because he wasnt accepting orders