The Astros and general manager James Click failed to reach an agreement on a new contract. Click rejected a one-year offer:

Conflict within the organization on baseball operations decision-making persisted throughout the Astros’ championship run this season, sources told ESPN, and Click’s reticence to accept owner Jim Crane’s one-year contract offer was the talk of baseball’s GM meetings in Las Vegas.

ESPN.com

I find this very odd, as it’s not clear where the conflict existed. The local Houston article has little else, except this:

USA Today’s Bob Nightengale reported that Click was “offered a one-year contract and raise from his $1 million salary on Monday, turned it down in pursuit of a longer contract, and was dismissed Friday after publicly airing his grievances at the GM meetings.”

Chron.com

I assume it will be fairly easy for Click to find another job, given his success with the Astros post-scandal.