When viewing 3D video, depth of focus does not change. That's the issue. 3D breaks the association between focal distance and convergence. It forces a constant focal distance while the convergence point varies. It's not normal for eyes to work this way, and it does cause disorientation, mild in some, stronger in others.
Whether this is a serious issue or not, time will tell.
Thank you for actually spelling out what exactly they were complaining about, and I can see how this would be an issue when viewing a monitor. However, you don't have to go to very large distance until the focal distance is effectively infinite.
I've played around with this lens approach for flight simulators, and I have to say that having the image near optical infinity makes a much larger impression than you might think. You are actually looking through the screen, not at it. The quality isn't great, but it greatly adds to the feeling of immersion. I think this is more important than 3D, since stereoscopic vision really only works at quite short distances.
Whether this is a serious issue or not, time will tell.