If a player is on the 40 man roster he needs to spend at least 20 consecutive days in the minors for it to subtract from his days on the 25 man roster. If he spends less than 20 days in the minors, it counts towards his days on a MLB roster. He did not spend 20 consecutive days in the minors yet, and therefore has not had any time subtracted from his days on a MLB 25 man roster.
Now, if he wasn't on the 40 man to start the season you would be right. Yet that is not the case here.