I saw it as well, at a store yesterday out on the shelf. It was marked as $49.99, but may be $37.99 like advertised next week. I have it coming from Amazon, but I noticed it on the shelf and made sure it was Season 2, and it was.
It's back available to pre-order now: http://www.amazon.com/gp/product/B00...-5846469?n=130 (Admin note - please do not include referral IDs in links.)
I watch the episodes first in order, then the special features. If there are commentaries I wait until I've seen all the episodes that season then go back and listen to those.
I noticed that as well. I pre-ordered it a few weeks ago before it was made unavailable, so hopefully there's no problems. I also noticed The X-Files thinpaks seasons 4 and 5 are unavailable the same way.