I don't think it's counter-intuitive at all! Here's what I'm interpreting from your comment:

* When you listened to expectations and met those expectations, you were reviewed as meeting expectations

* When you met expectations PLUS did additional stuff, such as "spending a lot more time understanding basic fundamentals of software engineering", you exceeded expectations.

Sounds perfectly reasonable to me! Especially since becoming better at SE fundamentals probably made you an objectively better programmer.