Can cis-trans isomers have same InChI?
Professor Jonathan M Goodman gave an explanation on the InChi mailing list:
https://sourceforge.net/p/inchi/mailman/inchi-discuss/thread/B7D99356-8B55-43BE-8C2A-B8CC3EB37799%40cam.ac.uk/#msg37289766
In summary, the given class of molecules represents a special case where the current InChi algorithm (1.06) produces less than useful results in order to being able to handle all other cases satifyingly. Prof Goodman hints at work being done in organometallics which may affect this behaviour. So, it's not a bug in the implementation of the algorithm, it is the algorithm itself that needs improvement.
The linked message also contains a smaller minimal case, confirming that it is the hetero-ion together with the keto-enol configuration causing the phenomenon.