Of course a system misbehaves if you use an (intentionally) broken application. That's a Google Chrome issue and not an issue with pinning.
You may argue that this is is broken behaviour, but that's what pinning currently is in browsers. Seems it's this way in Firefox too ("pinning not enforced if the trust anchor is a user inserted CA, default" - https://wiki.mozilla.org/SecurityEngineering/Public_Key_Pinn...)