I'm sorry, I don't quite understand what you mean by...
I'm sorry, could you explain what you mean by...
I'm afraid, I'm not really very clear about what you mean by... (tentative)
I'm sorry, but could you possibly explain what you mean by... (tentative)
Did you mean that...
Do you really think that...
Did you say...
But you said earlier that...
I don't understand what you mean by...
What (exactly) do you mean by... (all rather direct)