There are several topics about Owncloud already created. So I assume Owncloud somehow redirects the LE .well-known request where it should not.
Here are two topics:
Fortunately the latter is also solved and proposes a change in the .htaccess.
Maybe someone might take this instructions into the LE or the Owncloud FAQ or even change the default OwnCloud config. This would prevent this error in the first place.