"What was that?" means "What did you say?"

People don't ask "What did you say?" directly very often, because "What did you say?" can be used when you're really angry or upset about what someone said:

A: (Quietly) That's a stupid idea.

B: Excuse me!? What did you say!?

"What was that?", on the other hand, clearly means that you want to know what the other person said.

When you pronounce "What was that?" 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 can say "What was that?" in this way if you see something strange and you're not sure what it was.