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This is likely only for users who aren't email confirmed.
See: http://docs.webplatform.org/w/images/2/2e/comments-stacktrace.txt
I found a hook look in OutputPageBeforeHTML: Comments extension binds to OutputPageBeforeHTML. This in turn calls SemanticForms, which adds text to the wgOut object, which in turn calls OutputPageBeforeHTML. In order to fix it, I put a flag in the main rendering function in Comments that indicates that rendering is already in progress and prevents another execution of the hooked function. For testing, I created a new account and did not confirm any email. Then I went to the problematic article and added a comment. This worked for me. As of now, the fix is only applied to the test system. I'd be happy if someone else tests and confirms the bug is resolved.
Is this still an issue? I haven't seen any issues with the commenting system.