Last season when you signed him (to a ridiculously high amount for this caliber of player BTW), he was a minor league free agent, meaning that he had spent at least 6 seasons in someone else's minors without ever playing in the bigs and was left off the 40 man roster.
So now this season, the system sees him as a pre-arbitration player with 1 year of ML service time. Since he made $3.2M last season, the system automatically gave him the maximum pre-arb amount of $500k.