Learn Croatian: Ona razumije tri jezika. - She understands three languages.

This is the special rule for numbers! In Croatian, after the numbers two, three, and four, we do not use the regular plural. Instead, the noun takes the genitive singular form. Since the basic dictionary form is jezik, adding an -a gives us jezika.

I thought the direct object of a verb should be in the accusative case. Why is the noun in the genitive case here?

That is normally true for direct objects! However, numbers like 2, 3, and 4 act like a boss over the noun. The number itself takes the accusative slot, but it forces the noun following it into the genitive singular, overriding the usual accusative rule for that noun.

Does the number tri change its form depending on the gender of the noun?

No, the number tri (three) stays exactly the same for masculine, feminine, and neuter nouns when used as a subject or direct object. You only need to remember to change the noun that follows it.

Could we drop the word Ona and just say Razumije tri jezika?

Yes, absolutely. Croatian verbs have unique endings for each person, so the verb razumije already tells us it is he, she, or it doing the action. Including Ona just adds a little emphasis, like saying that SHE is the one who understands them.