I've seen issues like this a bunch of times. The causes have ranged from bad software/firmware releases to bad (or super-cheap) USB hubs; and even insufficient power to the Prusa's electronics. I would start by upgrading/downgrading the software and firmware first. Then try going direct to the Prusa from the computer with a good USB cable.
While it isn't cheap, we put all of our printers on beefy UPSs. It had a pretty big impact on issues overall. Our failure rates dropped to near zero.
- Todd
Todd Sampson