What kind of stones is the Torah referring to?
Rashi: It is referring to weights. 1
Whereas "Eifah va'Eifah" in Pasuk 14, is referring to dry measures.
What is wrong with having two different weights in one's pouch?
Rashi and Rashbam: The Pasuk is referring to where the two weights (do not complement one another but) clash with each other 1 - where one uses the slightly larger one for purchasing, and the smaller one for selling.
See Sifsei Chachamim and Rashbam.
Why does the Torah insert these Dinim 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 oneself. 2