Both Spirit (Mars) and New Horizons (Pluto) had down days as issues with file system management puzzled the IT staff.
The New Horizons case was a crazy mad-scramble, as the probe was scheduled to pass by Pluto in a few days whether the probe was working or not. There was no re-do. Dozens of choice careers were in the balance.
Probe chips are still not very powerful by today's standards because they are designed to work in the harsh conditions of space. Thus, they are more comparable to a 1980's PC, and may mostly stay that way, being smaller components don't handle radiation well.
I read somewhere it's estimated that even surface-reaching cosmic radiation fouls up the typical desktop PC roughly once a year. Most just grumble at Microsoft and reboot.
... has become a virtual impossibility in the age of short-lived consumerism and fad-driven development.
I've spent a lot of time since then looking into how to build reliable systems that operate for decades and... there are no easy answers. You have to have an amazing amount of knowledge about the engineering context (what's it like to run a computer in space), the scientific mission (IE, given this payload mass, what instruments can we fit), judicious software engineering skills (just updating the firmware on a machine that's millions of miles away is a challenging problem, worse yet if updating the firmware bricks your control plane), project management skills (to ensure you make your launch date), and the dedication to keep things going long after most people got bored of them.
After a long time playing with complicated systems I went back and played with 8-bit microcontrollers and they were actually really fun because it forces you to build systems that are reliable without a terminal and resource constrained (you'd have a hard time fitting a program as large as this comment into an arduino...)