The main issues seem to be consistency across vendors, occasional bugs in router software, that type of stuff.
There has been disagreements as well on how things should be implemented such as radvd vs DHCP6 NAT66 and so forth.
As a result there is a lack of universal practices which I think over time isnt helping matters, one that frustrated me recently is the "happy eyeball" mechanism added to Chrome (and anything based on chrome, which is a fair amount of software including steam).
Interestingly the actual RFC isnt as new as I thought it was.
https://www.rfc-editor.org/rfc/rfc6555Happy eyeballs has been used for a while in DNS, but once it was added for general session steering is what made me consider it going too far. Its currently not configurable and is unlikely to be in Chrome.
After the Chrome changed I was forced with reality of having to either filter out AAAA responses on my DNS server, or disabling IPV6 completely or blocking IPV6 via local firewall on my windows desktops for any software using the Chrome engine. I did the latter.
Firefox didnt adopt the practice so still behaves in a sane way honouring the OS routing prefix order.
Weaver, control panels like directadmin do already have a hold your hand approach for IPv6 although it does require server administrators to enable IPv6 on the server and assign a prefix to it. I think because it gives no SEO bonus, many wont care, as soon as google made https give points, many flocked to enable https on their web sites. There is also that dual stack adds another way for a site to break, so has an element of risk to it.