How are green OA publications cited?
If it's a direct copy of the published version (same PDF, with formatting, headers etc.) I'd be very surprised if anyone would fail to cite the journal version. I mean, what's next? Providing the address to their university library instead of using a standard citation format for a printed publication?

If it isn't a direct copy, but the copy in university repository B lists the journal reference, readers will generally cite the journal version. This also tends to happen with papers on preprint repositories such as arXiv, except when people find the preprint version before it's published, and don't remember to check their bibliography for updates before they submit/publish their own work. If no journal reference is listed, you can't really blame the readers for not noticing the version in A, so make it easy for them to get it right.

Now, this isn't really enforced. The closest thing I've encountered is that many journals will ask authors to double check references that don't look like peer reviewed and published versions during the copy-edit phase. As you say, this could be considered a disadvantage to green OA, but it's likely outweighed by the visibility advantage of having a non-paywalled version.