Not a bug, it's just a choice on their side.
Up to FIFA 16 it could be fixed with Revolution Mod (which allowed us to import custom kits over the default ones) but at the moment there's no solution for FIFA 17 unfortunately.
What I don't like, also for teams having licensed GK kits, is that they only come in a single colour (e.g. Seattle Sounders have a black GK kit in FIFA, while Frei also played in a white one
and in a lime yellow one
This means that when you play as Seattle against DC United, Seattle's keeper will clash against DC United's home kit for example.