Can cis-trans isomers have same InChI? From all we know only tautomers should get the same InChI key, or, in case of the second block, if there are lots of stereo centers. However these cases are just collisions, they still have different InChI. I have found a class of molecule pairs, with four real-world examples in ChEBI and PubChem, where both web input pages of ChEBI and PubChem generate identical InChI and keys, despite there being a different E-Z configuration on a double bond. And these are also entries in the said databases. My question:
Is this normal/expected? Is it a bug in both software, which part of it?
The pairs:

5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-1-benzopyran-1-ium-3-yl 6-O-[(2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside and 5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-1-benzopyran-1-ium-3-yl 6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside

2-(3,4-dihydroxy-5-methoxyphenyl)-5,7-dihydroxychromenium-3-yl 6-O-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside and 2-(3,4-dihydroxy-5-methoxyphenyl)-5,7-dihydroxychromenium-3-yl 6-O-[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside

5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)chromenium-3-yl 6-O-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]--β-D-glucopyranoside and 5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)chromenium-3-yl 6-O-[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside

5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)chromenium-3-yl 6-O-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-β-D-glucopyranoside and 5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)chromenium-3-yl 6-O-[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]-β-D-glucoside-glucopyranoside


Addendum: I also confirmed with two different SDF files that the current inchi-1 Linux binary generates the same InChi.
P.S. This is a pair of minimal molecules:

Both have the InChi InChI=1S/C11H10O3/c1-14-8-11(13)7-4-9-2-5-10(12)6-3-9/h2-8H,1H3/p+1. If the methyl is removed, leaving a =OH+ group at the end, both isomers get different 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.