Mechanical failure caused a malfunction in Jim's pod and woke him up.
The Avalon, a sleeper ship transporting 5,000 colonists and 258 crew
members in hibernation pods, is on course to the planet Homestead II,
a journey taking 120 years. Thirty years into its journey, the ship
passes through an asteroid field, leading to a collision that causes a
malfunction. The malfunction awakens one passenger, mechanical
engineer Jim Preston, 90 years too early.
Another POV I found from Quora,
As I understood it from the end of the movie, the opening scene
represented an encounter with an asteroid field that overwhelmed it's
defensive capabilities. The “deflector dish/asteroid destroyer” device
could keep up with the smaller pieces, but was unable to stop a large
piece from penetrating into the ship. This large asteroid, though
primarily destroyed, had some smaller pieces slam into and through the
Avalon, and damaged the reactor control computer. Without anyway to
repair it's damaged reactor control computer, the ship began to use
computer resources from other less necessary systems, beginning with
the computer control of Chris Pratt’s sleep chamber.