The issue was never "Microsoft has a monopoly on IE6". That's obviously nonsense.

The monopoly that Microsoft held was the home computer operating system market, first through DOS, then later through Windows. Holding a monopoly like that isn't illegal unto itself. What they were actually found guilty of was unfairly leveraging their monopoly on the OS market to gain the upper hand in a different market (the browser market). The subsequent range of issues we had with IE6 (compatibility, security, etc) was a result of Microsoft succeeding in achieving a monopoly on the browser market through illicit means.

Likewise, "Apple has a monopoly on the App Store" is just the same amount of nonsense. What you could argue is that Apple has a monopoly on the home computer market, or the mobile phone market, and that the way they integrate the App Store should be considered illegal leveraging of that monopoly, but that argument simply doesn't hold water — Microsoft's monopoly on the OS market at the time was pretty much incontrovertible, you simply couldn't walk into a shop and buy a computer running something else (except maybe a Mac at a more specialised place). Today, just about any shop you walk into that sells computers will probably have devices for sale running three different OSes (macOS, Windows, ChromeOS). Any phone place will have iPhones and Android devices, and probably a few more niche options. Actual market share percentage is nowhere near the high 90s that Microsoft saw in its heyday. At most, Apple is the biggest individual competitor in the market, but I don't think it hold an outright majority in any specific product class.

Mind you, I think that there is a good argument to be made that the Apple/Google duopoly on mobile devices does deserve scrutiny, but that's a very different kettle of fish.