If the author in their submission of the manuscript hadn’t identified the prior licence which will apply to any AAM arising from that submission, or that they were funded by a member of cOAlition S then, we accept that the author hasn’t taken all the steps requested of them and that the publisher has dealt with the manuscript without there being a clear notice of the prior CC BY licence to the AAM.
Assuming the author self-archives the AAM in a repository, an issue is only likely to arise when/if the publisher challenges the presence of the AAM on that repository via a take-down notice. We hope that once the publisher was made aware of the author’s oversight, that they would respect the obligations the author was under with their funder and withdraw the takedown notice. It is unlikely that a funder would encourage a repository to resist such takedown notice if the publisher want to pursue the matter.
However, if an author, in their submission, makes it clear that “this work is funded by (for example) Wellcome”, we would rely on the fact that publishers have been told that CC BY licences apply to AAMs from Wellcome funded authors (despite the words CC BY having been omitted), and as such we would help resist a take-down notice on the basis that the publisher did have knowledge of the prior licence.
As, in this example, the researcher has not fulfilled the requirements of their grant conditions (i.e. by making it clear to the publisher than any AAMs arising from their submission is already licensed CC BY) It would be a matter for the particular funder to decide how to address the breach of their funding conditions by the author.