I’m no expert, but I think “you’re already” doesn’t work because the “anti-stress” on the contraction tells us the focus is later, but the focus of “already” is actually on the “are” in “you’re”. It trips us up because it sneaks the focus past us and then just ends the sentence before the focus the stress told us about arrives.

It may also be because “you are already” is a variant of the sentence “you are” which can’t be contracted, so the contraction insinuates “you’re already [something]”. It makes us parse a different sentence structure than it is, then we get confused when the sentence ends early.