You're talking with your friend on the telephone, and the signal is breaking up. She said something, but you didn't hear what she said. You ask:
What was that?
What was that?
This question means "What did you say?"
People don't ask "What did you say?" directly very often, because "What did you say?" can actually be used when you're really angry or upset about what someone said. "What was that?", on the other hand, clearly means that you want to know what the other person said.
When you pronounce this phrase, the stress should be on the word "What":
What was that?
Don't stress "was". If you stress "was":
What was that?
...it expresses the meaning of "That was strange!" You ask this question when you see something strange and you're not sure what it was.
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