You are right that it is a case problem, however I am syncing onto a ZFS pool which is case sensitive (OpenZFS on OS X 1.9.0), so that should be allowed? It seems like it is detecting them as duplicates even though they are in fact not duplicates and should be fine on that FS.
I also tested, I'm able to create 2 files which only differs by case just fine on the pool.
Could it be that rclone cannot properly detect the case sensitivity on that configuration of filesystem?
rclone assumes that everything on OSX is case insensitive. It isn't easy to detect whether a file system is case sensitive or not without writing a file to it, which I considered but decided that it would be unexpected for the user.
I made a beta with a --local-case-sensitive flag in this beta which overrides that default - can you give it a go?