What kind of stones is the Torah referring to?
Rashi: It is referring to weights. 1
Whereas "Eifah v'Eifah" in Pasuk 14, is referring to dry measures.
What is wrong with having two different weights in one's pouch?
Rashi: (Both are allegedly the same weight, e.g. a kilo. The discrepancy is small, and not overt.) He uses the slightly larger one for purchasing, and the smaller one for selling. 1
See Sifsei Chachamim and Rashbam.
Why does the Torah insert these laws here?
Seforno: After dealing with Mitzvos that concern bringing the Shechinah down to Yisrael (and of causing its withdrawal 1 ) the Torah is teaching us that it is not only the actual perversion of justice that Hashem hates (and that causes the withdrawal of the Shechinah), but even the retention of vessels with which to cheat - and from which one should therefore distance himself. 2