Hi @mariesheilag,
I don't know whether this is related to your problem, but cert-manager versions have serious bugs in their Let's Encrypt integration—so serious that Let's Encrypt is planning to block everything prior to 0.8.0 this autumn.
Since this blocking hasn't been implemented yet, it's not itself the reason for the error message that you're seeing, but this is an important indication that your cert-manager should be updated to a newer version.