I disagree respectfully in this instance for my case in particular. Here is why, for me this issue is new to iOS 9. It was not present in any of the betas. It is apparent after the animations end, not durning which I understand was changed in iOS 7. My wife has an iPhone 6 that is not upgraded to iOS 9 and when doing a side by side comparison there is no "missed touch". I am very in tune with my devices and noticed this the very first time I unlocked my phone after the upgrade. Others may have had something similar in the past, I don't discount that however this was obviously apparent to me right away.
Hmm, I'm not sure if the behaviour was different during the betas, but it doesn't seem to have changed significantly across iOS 7/8/9 where any touches which begin before the unlock or app switcher animation end are ignored. I tested this on an iPad on iOS 8.3, and this video comparing iOS 8 to iOS 3 seems to show similar behaviour, albeit in the video he's mad swiping instead of just doing one long touch (like in cynics's video):