Why cuáles & qué were used here, and not only one for both sentences?

Why cuáles & qué were used here, and not only one for both sentences?
 

"A ver si puedes identificar qué palabras son masculinas y cuáles son femeninas"

qué was first used then cuáles. Why not both of them are qué or cuáles?

Because we're edgy about repeating words. ;)
Although it's a rare case, both words work in this sentence, so it was easy to avoid repetition. :)

The word 'qué' is an interrogative pronoun meaning 'what' or 'which'. It doesn't have a plural form, so it can be used whether it is followed by a singular noun or a plural noun. Note that it precedes a noun.
The word 'cuáles' is also an interrogative pronoun meaning 'what' or 'which'. It is used when a verb follows. It has a singular and a plural form. In your case, it agrees with the subject complement (the predicate adjective 'femeninas') following the linking verb 'son'.

There are times when 'cuáles' is used instead of 'qué'.