No idea how to prevent the issue, but I've been caught mid sentence before and accepted installs, upgrades, random popups, etc. Ones from Skype tend to be the most infuriating / scary..
We looked into this while I was Trolltech. Decided against doing it for Qt unilaterally, it's really something the system must do, or else it's too annoying.
They are just tidying up parameters for a bit of post constrast injection imaging. They hit enter to accept a parameter change just as a notification appeared to trigger the next scan. Basically it missed the key imaging phase and the scan had to be repeated a day later once the injected contrast had been cleared out of the patient’s system. Imaging equipment vendors seem to make custom UI in places where it is unneeded (software buttons which trigger on touch down, not touch up for critical functionality?! Why?) but in places where it would be safer to make something custom they don’t.
Edit: a possible exception being the “please enter your iCloud password” curse I somehow cast on myself sometimes.
Return is a dangerous key!