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Thermite aren't flyers, nor were they patched for invasion. Those are Skimmers. Thermites look like the regular mites, except they role into a ball and explode.
Out of curiosity, has anyone tried to blow up the turrent you can use in DC? Likely the missing enemy is just a glitch; if you do play invasion long enough though...the latter end levels (specifically in Serenity) have some of the older enemies from TCON make an appearance that otherwise don't show up in C2's campaign.
One I'm thinking of in particular is the old TCON end stage Bunker Cyborg. They had Torsos that sorta resembled c3po but with angry looking helmets/faces.
again, this likely isn't what OP was missing; figured I'd throw it out there anyway.
A big part of me tries very hard to behave. A small part of me laughs at the effort and behaves like an ass, anyway.