What the agent should have done is scanned your US passport, not your foreign passport. As a US citizen you are supposed to leave on your US passport. What you use to enter the other country, the US doesn't care as much, and showing (but not letting the agent scan) your foreign passport would have been sufficient for the agent to issue you a BP.

To enter your home country, you could have used either, although your home country passport is probably less of a hassle in terms of lines, etc. And, of course, your country may have similar regulations to those of the US, in which case you have to enter with your home country's passport.

In the end, I don't think it will be a big deal, when you re-enter the US you will certainly use your US passport.