I've seen Harper sign a cheap, short deal in one of my leagues too. He signed a 3-year deal w/ San Francisco w/ an average salary of $19m...
Just a shot in the dark, but I wonder if Qualifying Offers play a part in this.
1. The QO system doesn't seem to reflect real life. IRL:
A. The amount is the mean salary of MLB's 125 highest-paid players, yet, in the game, the dollar amount of a QO is always $15m. I don't recall ever seeing it change to reflect the mean.
B. For a player to receive a QO, he must never have received one previously in his career, yet, in the game, that's not the case. I once offered a player of mine a QO, he accepted it at $15m, but the following offseason, I was given the option to offer him another one. I didn't because I knew he'd likely accept it again, but didn't want to pay him $15m for another year.
2. Considering the QO amount is always a static $15m, it's just too easy for clubs to get compensation for impending FA's, which leaves me speculating if players aren't being signed quicker because a comp is attached to too many of them and teams aren't willing to give up draft picks for them, even for 1 year deals:
A. High quality RP's like Britton, Chapman, Kimbrel, etc. will always have a comp attached because their demands usually exceed the $15m QO. If he's still pretty young, he'll reject it even if his demand is less (i.e. Mark Melancon's 33 w/ a $12m demand and he rejected a QO)
B. Adrian Beltre is currently a FA in my league. He's 39 and demanding $16m a year, but has a comp attached, meaning he obviously rejected the $15m QO from Texas. The way it stands in the game, from what I've seen, any player w/ a contract demand over $15m will almost assuredly reject a QO. Would a 39 year old reject a 1 year, $15m deal IRL? Highly doubtful. So why would I, even as the Braves who need a 3B and a $40m offseason budget, give up a draft pick for a 39 year old?
C. It's the first day of '18 free agency in my league and there are 20 players w/ a comp attached. IRL, only 9 players were offered QO's in November. The year before, 10 were offered QO's and 2 accepted, meaning only 8 hit the market with comps attached.
If all of this is factored into the in-game free agency process, then it's no wonder why there are so many weird FA contracts...