You can probably begin to get to the bottom of most internal Emacs problems with debug-on-entry. This function prompts for a function name interactively (which also hooks into helm) and will essentially set a breakpoint within Emacs on that function. When it is called you’ll get to see what functions were called and with what arguments.
But you can use debug-on-entry on the offending function (which you should be able to find in the messages buffer) to set a breakpoint and walk up the stack to see if you can understand the problem better. It was interesting in my case but didn’t solve the issue, I just commented on the GitHub mirror of the commit and the author fixed it for me. Open source rules.