It seems that both Apple and Microsoft prohibit GPLv3-licensed software in the app stores for their locked-down devices (i.e. iOS, Windows Phone and the Metro part of Windows). I have heard various explanations for this. However: Would they even be able to allow this license in their app stores if they wanted to, or does the GPL's anti-tivoization clause already prohibit this?
Apple effectively ban any GPL because they only allow redistribution through the store and by registered developers. So if you distribute the GPL to your users they cannot abide by it.
Apple could simply allow any GPL app to be redistributed by any user through a free section of the site - but chose not to. Ironically OSX is based on a free BSD Unix kernel.
Microsoft have an historical objection to "the cancer of open source" and their licence explicitly bans any open source licenced app that requires redistribution of source (ie GPL). This is their right, it's a business decision - just like banning sales in a particular country. As their position in the market becomes less dominant they might change their mind