You misunderstood the description, and EA help misunderstood you, I guess.
"Buy two, get one free" means that you are effectively only paying for two trooper appearances: the appearances are 20k each if bought separately, but the crate is 40k, and it contains all three available skins (so logically it should cost 60k credits without said discount).
I'd guess that by "buying them at the same time" they meant that you need to buy the crate to take advantage of this discount, instead of buying the skins one by one through the Appearances menu.
Well, actually, I didn't buy them individually. I bought the two bundles expecting to get the third "free" one. I've come to the conclusion that it's a glitch in crate bundle menu.
I think you still don't understand. There is no glitch, you were never supposed to get a free crate.
The description means that in each crate, out of the three appearances it contains, one appearance is free - since you don't have to pay 60k, only 40k credits.
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