I'm a biochemist. One of the units we occasionally use is LD[SUB]50[/SUB]. It describes the lethal dose, usually in milligrams of compound per kilogram of subject, to kill 50% of a population given that compound. Let's say that I'm studying a new pesticide, and initially see a LD[SUB]50 [/SUB]of .005. Assuming my pests are 1 kg, that means it only takes 5 micrograms to have a 50% chance of killing one! That's pretty lethal.
A week into my analysis, and the pests grow resistant to my pesticide. Now my apparent LD[SUB]50 [/SUB]is 0.25 mg/kg. Oh no! My pesticide didn't change at all. However, I still need to adjust the unit I use to describe it. I could try adding a fudge factor to my calculations to account for the change, but the clearest way to express the difference is by changing the LD[SUB]50[/SUB].
TLDR; the egg heads making the missiles told you they aren't working well using a clear and established measurement. It would be inaccurate of them to insist that the missiles are still effectively penetrating the Thargoids armor.
That's fine, but the penetration value is not inherently exclusive to interacting with the thargoids. So it's not that they got resilient, it's that the pesticide just became worse in itself.