I agree with Rusty.
Also, to me, it kind of elides a word to make a "more complete" sentence:
- ¿Dices que lo reconociste? -> Are you saying you recognized him?
- ¿Cómo que lo reconociste? -> ¿How is it that you recognized him?
- ¿Es que lo reconociste? -> Is it true you recognized him?
In Mexico you're more likely to hear "¿Lo reconociste?", but in other regions and in higher registers the "que" is added naturally.
Side note: There is also:
- ¿Qué, lo reconociste? -> So, did you recognize him?
