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.