You can remove a guy from your 40 man (as long as he has options) without passing through waivers.
(1) Designate for assignment without waivers.
(2) Submit move
(3) Re-assign him to minor league team
(4) Submit move
(5) He's now back on the same team, off 40 man
It's a bug because it makes it easy to add guys to your 40 man before rollover or before Rule V draft, then take them off without risk of losing them.