I wasn’t trying to imply that contracting is always wrong. Rather, it is not always right.

In the case of “it’s what it’s”, the “it is” part is being stressed, so contracting it is weird.

This is why I find contracting “You are already“ weird. To me, the stress is on the are. However, after reading and re-reading the statement in my head, I can feel people stressing the already instead. To those, “You’re already” would probably be fine.