Strange! We're looking into this, but so far can't reproduce the error. Does it show up in the logs? or on the page? or both? Is that the complete error?
The Cloner doesn't actually have that exec() command in it. And it never calls "cp -r". Was that something you added? It only calls php copy() which is not recursive. We wrapped it in our own recursive function, so "cp -r" isn't something that the cloner would be generating. Neither is "/*" at the end of you origin path because it recursively scans and copies the files and directories one at a time.
Anyway, happy to help, but still shooting in the dark here. Let us know what additional details you can provide, thanks!.