A 10 min talk with 3 minutes of actual Q&A is no worse for the scheduling of the conference than a 12 min talk with 1 minute of actual Q&A. And a 10 min talk with 5 min of Q&A is better for scheduling than a 12 minute talk with 5 min of Q&A. -- So I wouldn't worry about schedule flow when you're asking about giving a shorter talk.
Going too long is an obvious problem -- if you're too long you short-change other parts of the schedule. Going too short isn't necessarily an issue. You either leave more time for Q&A, or you give people a slight bit more time to discuss things privately with their neighbors.
Instead, I'd worry about the content of your talk. There's a certain expectation of "substance" for a 12 min talk. Depending on your presentation style, you could hit that at 12 minutes, but you could certainly also be efficient and convey all that in 10 minutes. There are also people out there who could drone on for 20 minutes and still not reach that point. The issue with short talks isn't the time in and of itself, but rather that it's harder to put enough "substance" into the limited time period.
Note that "substance" here is effective substance. Rattling off a bunch of facts in rapid succession isn't effective substance, as no one listening can take it all in. You need to be able to communicate the substance, and that actually may involve presenting less, but slowing things down such that the audience can actually take it all in properly. But on the flip side, slower isn't always better. A concise delivery of points can be more effective than a detailed belaboring.
My recommendation would be to look at your presentation not from a time perspective, but from an effective communication perspective. Did you manage to cover enough "substance" in your talk for a 12+3 timeslot, or was it too thin? Was your delivery an effective communication of that substance, or did you hurry through it too fast/too ineffectively?
It's sometimes hard to gauge from the podium, but the attention of the audience is often a decent proxy. If you've covered the points you want to, and the audience is engaged throughout, then you've done well. If they've checked out at 7 min because they can't follow, that's bad. (If there was someone in the audience you trust for honest evaluation, I'd ask them for their opinion.) You can also sometimes get a sense of how the presentation went from the Q&A. If there's a bunch of basic questions you covered in the talk, then you may have gone too quickly and lost a bunch of people. If there's basic questions you didn't cover, you need to add detail. If there's a fair number of interested, advanced questions, you've probably done well. If there are close to no questions, then either you've bored everybody (so they no longer care), confused everybody to the point where they're afraid to ask questions, or did such a great job that you've addresses all the issues. (The last tends not to happen in practice.)