Had a read into permissions, and it looks like a lowercase ‘s’ sets the groupid permissions.
setgid has no effect if the group does not have execute permissions. setgid is represented with a lower-case “s” in the output of ls. In cases where it has no effect it is represented with an upper-case “S”.
I ran chmod -R ug-s /invoiceninja which has resolved the permissions problem and I have been able to update successfully.