Two to three hours late is not unusual for an Amtrak long-distance train. Among other potential obstacles, the California Zephyr traverses one of the snowiest places on the planet (Donner Pass). The best way to enjoy stress-free travel on Amtrak long-distance trains is to have no commitments on your arrival day.

It looks as if the westbound Zephyr has averaged 42 minutes late into Emeryville over the past month. Historical information is available here: https://juckins.net/amtrak_status/archive/html/home.php