Yeah, this is what tipped me over to believing that Freddy hit him with purpose.
Contreras gave a classic fastball inside sign and then some other motion, looks like a fist. Levering even remarked on it saying, "Going the old traditional signs." Video here.
Why is the catcher giving an old school sign? That's not the norm anymore. I doubt there's a button on the communication device that says, "Taladra a esta perra."
Anyway, I agree with the other poster that said even if it was intentional it seemed pretty mild as far as throwing at guys goes. It wasn't obvious in the moment, maybe there was some chirping on the field after the Siri home run earlier that tipped the ump off to something but the umpire jumping directly to tossing Freddy out wasn't really something I think most viewers would expect. Seems to me giving a warning would have been enough.