What are you referring to here? The only fights with aliens occurs in the Precursor System and those aren't that hard. Unless you tried to jump the dreadnought in the Dyson Sphere, but those guys are neutral and just want you to leave.

That dreadnought was too tempting a target and I just had to have a go at it :p It took a goddamn miracle to pull off, but I lost 5 ships in the process - and all I got for it were a bunch of alien guns and turrets. Turrets which will never be able to be mounted, because Joseph is the only freaking character with the Alien tech perk and he leaves as soon as this mission arc ends. Bah.

If you're talking about the Star Hammer Memorial that fight isn't too hard either, the aliens only start spawning once you damage the memorial and quit spawning once you destroy it. My problem is getting the memorial to drop at least 2 Precursor Guns, otherwise I'd have to wait until the endgame when Ternie comes back to harvest those ships she can summon.