I think the deer on my Xbox still make noise. But sometimes when two sounds happen at once, one overrides another. Perhaps that's what happened to you.
The wolves are still silent on the consoles.
And no, this is not the first game to have patches cause new bugs. It happens pretty much all the time with every game. (it's just unfortunate when they get left unfixed)
The wolf issue (lack of howling) was introduced with the Dawnguard DLC. There is no fix on the consoles, but the Unofficial Dawnguard Patch does fix this for PC users.
As far as I know, I've never had any issue with the deer not making the correct noises.