Well I don't know if I'd call that a debunking. The experiment could obviously be done better, but even this 'debunking' isnt denying that the environmental factors he was testing were responsible for the behavior. Yes humans are going to react differently in some situations, being more complex social animals, but we do see higher rates of homosexuality, and lower reproductive rates in more densely populated areas

Space. The areas were small even for rodents.

The 'behavioral sink' appeared well before the space was filled, and much sooner than he anticipated. This is generally attributed to the fact that unlimited food was airdropped in. These rats did not require a great deal of cooperation or social roles to perform their survival tasks, It was the younger rats without any social roles to take up that initially exhibit the ungainful behavior. I'm not 100% sold on the 'space' but if anything this just reinforces Calhoun's theory that the environment caused these problems rather than refuting it

Lack of recreation for the rats. Today we know that most mammals and birds require entertainment

This seems a dubious point. Precisely what form of rat entertainment were these mice deprived of that they would have in the wild, or even in their normal lab confines that don't exhibit a behavioral sink? But in any case, this still supports his narrative that the environment caused these problems, which was his whole point, again, not sure how this is supposed to refute it

Incest. As mentioned above the genetic diversity wasn’t the best and could lead to some pathologies.

This is extremely common. His other rat stock not in the controlled 'universes' would have been just as inbred, and this behavior is not normally seen even in known inbred strains of lab rats such as the F344. Even outbred wistar rats have this problem. If inbred rats commonly exhibited this type of behavior in any environment, the results of this study would not have been considered surprising

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329512/