It took me almost 4 years to come to the following conclusion: It is a camera issue (or rather a camera model issue) and it definitely isn't rare. Many reviewers call it erratic autfocus or just autofocus issues.
Looking closely at the pictures reveals that even seemingly focused ones while fitted to screen ("in the print size") are slightly out-of-focus while others are perfectly focused.
FujiFilm XF10 compact camera and Pentax DA-17-70mm-F4-SDM lens are good examples of an erratic auto-focus.

How do I prevent these spoiled images?

You can't. But there are some mitigation tips.

1. Repeat shooting the scene (if applicable). Ideally try to focus different objects in the same distance and then recompose. Choose the best.
2. Avoid focusing on glittering objects.
3. Back up with manual focus. You'll probably lose to perfectly auto-focused image (especially with short focal lengths) but you won't probably get a completely spoiled image.
4. While shooting panoramas, focus on the object that's known as the most reliable for your autofocus, then switch to manual focus. Check the last image after shooting.
5. Know your camera (or lens). Spend some time training with various focal lengths, apertures, focused objects, light conditions etc. to find out strengths and weaknesses of your autofocus.

Possible causes of erratic autofocus
Disclaimer: This is a speculative part, based rather on my observations.

1. Glittering objects. Even when out-of-focus, as they're "blown", these cause contrast enough to satisfy the automatics.

2. "Noisy" bokeh. It adds enough frequencies for the auto-focus to snap while better focusing is still needed.

Are there any lenses completely free from that problem?

I doubt that. There are excellent lenses with a very low rate of unfocused shots but even here you can't be 100% sure that there won't be a failure when you need it the least. Reshoot the very important scene even while using these reliable lenses.