quelli means those 'ones' when there is nothing else for it to modify. In this case, there is nothing to modify (quelli refers to the special flights ...) so indeed, it means 'those ones'. But we often omit 'ones' in cases like this because it is immediately linked to 'special flights'. Si?
Hm. In this case 'ones' seems redundant. I found this strand about 'these ones' and 'those ones' very interesting, if not at least chock full of differing opinions.
I agree with Laithmore. The English translation is very stilted. As an English speaker I would say either "those flights are special" or "they are special flights." The Italian word "quelli" suggests the former, just as "loro sono" or simply "sono" would infer the latter. I've come across many examples where a similarly turned around translation is accepted, so I think Duo is being particularly harsh in marking "those flights are special" as incorrect. Especially as it contains the same four words as "those are special flights" - just in a different order. And both mean exactly the same thing.