In the April 2012 issue of Superboy number 6, Superboy meets Supergirl for the first time when she encounters him suddenly. I am not totally familiar with the Superboy New 52 series, so this issue is sort of a mystery to me.
In Superboy issue 6, he realizes that he is a clone made by an organization called N.O.W.H.E.R.E. so he could be a weapon. Superboy meets Supergirl when she stops him and questions why he has the S symbol on his chest. She touches him to make him understand Kryptonian (which is similar to how Starfire learned English). Bridging communication, Supergirl decides to beat the crap out of Superboy, assuming bad intentions.
Although it is exciting when Superboy meets Supergirl, the issue is really a building point toward some more exciting enemies and bad guys and stuff. Superboy 6 shows its age by being marked $2.99, which was before the $3.99 price-hike that pissed everyone off. Its two-page center advertisement is for Batman Arkham City action figures, based on the popular video game of 2012.
The artwork of Superboy 6 could have been better in my opinion, particularly in a couple full-body panels where the two of them look like children. It is also apparent that the penciler did not supply much for the colorist to go on.
If you are interested when Superboy meets Supergirl for the first time and want to experience their confrontation first-hand, be sure to pick up (Affiliate Link) Superboy 6 (New 52 version) yourself.