My baby goes potty in the powder room when we don't get her out in time
Yorkies are extremely intelligent and vocal.
I agree with everyone that he is trying to tell you something.
Kinda like a baby or young child that understands what they are saying,
but it's up to you to figure it out.
You mentioned that you put him in his crate for 'time-out'.
I'm trying to help here, not criticize, so please understand my intentions.
That said, their crates should be their safe havens, castles, homes and very special places -
try not to put him there as a form of correction or criticism.