First, notice the short vowel on “were”, because it’s unstressed. This is often a surprise for learners. The really interesting thing here is the intonation though. Notice how the stress is made by a drop, instead of a jump in pitch, followed by a rise, instead of a fall. This is because the phrase refers back to something the other speaker just said.
The phrase has slightly different meanings, depending on context; for example, you could simply be asking someone to continue after an interruption, but it might also be because something happens to confirm or disprove what the person was saying:
A: “I don’t think it’s going to rain today.”
It begins to rain hard.
B: “You were saying?”