I'm not really clear on your question, but from what I think:
B doesn't understand something/B thinks C doesn't understand
something, and interrupts A, to clarify.
If this is the case, then both your sentences can fit in a given context.
If B doesn't understand what A says, and says this to C , then this sentence would fit:
What is Mr. A trying to say?
If B doesn't understand what A says, and B expresses this to C, along with some other meaning too, then this sentence would fit:
What Mr. A is trying to say doesn't make sense.
The reason I added along with some other meaning too is because the following sentence doesn't stand on its own, and needs some additional meaning to it:
What Mr. A is trying to say?
If my answer doesn't explicitly answer your question(s), perhaps you could edit and reword it to make the situation clear.