I have tested several workarounds to disable the annoying magnifying glass with css, but on my iOS9 meteor cordova build it appears for a moment and fades out after
Yes, it is related to iOS9. Since you are a Cordova user, this plugin will fix the problem for you: https://github.com/EddyVerbruggen/cordova-plugin-ios-longpress-fix
It has to do with the UILongPressGestureRecognizer executing before handling the -webkit-user-select: none in your css.
I hope this helps you out.