Already today, it is not very easy to bring a computer into space, even with our (relatively speaking) very primitive silicon based Boolean logical computers.
On the ground we are spared the threat of cosmic radiation of most sorts because the atmosphere provides a thicket of annoying air molecules that get in the way of such rays before they have the chance to reach the silicon chips and play with them.
In space it is a different matter. There you have a diverse population of subatomic particles that make up a "colorful" spectrum of cosmic radiation. And these particles/rays do bad things when they get into a silicon chip. At worst they will actually start destroying the semiconductor components. At "best" they will saturate instruments (which is how we discovered that space is teeming with these things in the first place) or start flipping bits on your hard drives and/or volatile memory, zeroes becoming ones and vice versa.
And considering how we discovered the Van Allen Belts just very recently, despite them being right in our proverbial back yard, who knows what interesting things we will find when we get out into space for real. We still have no idea for instance how Dark Energy and Dark Matter behaves. And we cannot say for certain that the laws of nature are actually constant or if they will start behaving queer once we get out into the wide black yonder.
Thus you can hand-wave it like so: just as Explorer 1 went bonkers once it actually got out there, due to radiation we did not really expect to find (even though some scientists had predicted it), invent some kind of radiation that does something similar with your quantum computers. A phenomenon that for the moment is being researched but that is poorly understood by the time your story is set. Patches, areas or even whole regions beset by this radiation would provide excellent plot hooks for you, a well of different scenarions that you can choose from.