It's got errors, as others have noted. It's awkward, has a missing word, and contradicts itself (once he's been there a bit, then instantly?). I'd recommend rewriting it completely.
Once he was in the office a few minutes, Jake instantly noticed that several of his co-workers, who were usually very at this time, were missing.
After a few minutes in the office, Jake noticed several co-workers, usually there by this time, were missing.
Shorter, tighter, clearer.