I've never seen a dualstack connection cause breakage. And if it does break with IPv6 support being available, then it's the developer's fault. Instead of disabling IPv6 you should alert them of the problem and if possible use an alternative service, which supports IPv6.

In the case of Humble Bundle breaking, it seems simply because some of their CDN subdomains are IPv4-only. Since the site loads various resources from those IPv4-only endpoints, it causes everything to just break when accessing over IPv6. In a way I'd argue it's still better than your browser displaying "no valid IP address for this domain" – usually you can at least find an e-mail address at the bottom of the page to alert them to the problem.