In Australia,they found that some languages____having only a handful of speakers left.(A)be down to(B)to be down to(C)were down to?

The answer is (C) were down to.

"down to" = 只剩下少量數目 (下接名詞 ~ 的東西)
"having only a handful of speakers left" = 只剩下少數幾個說這些語言的人

Note: 
(1) "find" does not fall in the category of the verb group (suggest, advise, order, demand,...) that makes the main verb of its object that-clause to use "subjunctive" form.  Therefore, "be down to" is not the answer.
(2) the object of "found" is the noun clause "that some languages were down to ..." but  not "some languages".  Therefore, "to be down to" is not the answer.

find(language) to be down to (v)
find (that) language were down to.(x)