Well, I mentioned the two that I am most keenly aware of. I only know what I've come across, so I'm assuming there's lots more.
To my knowledge, file downloads worked in all browsers prior to mobile Safari being initially released. So Apple did release a browser that broke some quite basic web functionality.
I don't know how I missed that part of of your post. Sorry about that. Still. I find it quite a stretch to argue that not supporting file downloads "breaks" the web. Users don't perceive websites to be broken just because they can't download files. It would be akin to claiming that a device with no camera breaks the web by not supporting the camera API. Or that the Lynx browser breaks the web by not supporting CSS and JavaScript.
Regarding Apple's insistence on not supporting Ogg (Vorbis|Theora) (I assume that's what you're alluding to), those codecs were briefly recommended by the HTML5 standard, but were later dropped.[1] Again, I think its a stretch to say that Apple broke anything, simply because they resisted a proposed standard. I know a lot of developers were disappointed, but that's how committees work: You don't always get it your way.
To my knowledge, file downloads worked in all browsers prior to mobile Safari being initially released. So Apple did release a browser that broke some quite basic web functionality.