Crying when waking up in crib

My baby has been in his crib in his room since 6 months. Since around that time he has been waking like every 3 hours again. The first night or 2 he slept for several hours, but not since then. He did get sick around that same time, but was better in about a week.

Every time he wakes up in the crib he cries...a very sad, kinda scared cry. Not just a fussy wakeup that turns into crying. It's like it's the first time he's ever been in there every time he wakes up. He crawls to the corner or puts his face on the slats and just cries.

We have been bedsharing here and there the last month or so, but he did this even before we ever had.

Any thoughts?