Ok, so, quickly posting details of this bug, so that if anyone else experiences this they understand why they cant use their mount utility skills with hotkeys with certain settings.
Anet allows you to set mount skill 1 and mount skill 2 with any hotkey binds, which means you can use any hotkey including the hotkeys you would have otherwise used to bind to your utility or weapon skills.
This said, the "hotkey is already bound" warning will not occur when a new mount utility skill is added, which coincides with your utility skill hotkey bind and a mount skill bind.
In my case, I have utility slot 2 bound as "C". I bound mount skill 1 also to "C" because the game at the time let me and didnt give me a warning.
When I learned mount utility slot 2 "bonds of faith" it defaulted to use hotkey "C". Since I previously bound "C" to mount skill 1, use of C was limited to mount skill 1 and did not execute mount utility slot 2.
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