Wait, really? Could you share some examples? Why would they break for a FQDN. Wouldn’t that mean that the root servers aren’t configured correctly for that TLD?
I'm not sure exactly why things break, but as an example: fully-qualifying youtube.com (to youtube.com.) used to break the code that displayed the ads and you could watch ad-free
People get confused (particularly in the US) if they are always used to x.y.