I am using rsync to make a duplicate of an ExFAT-formatted external HD to another external HD. At the end of the copy, I got a message saying some files had vanished during the copy. So I used diff to see what files weren't copied. There are a lot of files starting in ._ that weren't copied, so I'll try using dot_clean to fix those and re-copy. But there's another weirder problem.
Diff tells me a certain file exists 'Only in /volumes/[...]' so I go that directory and do a ls -a and that file doesn't show up in the list. I do a diff again and it again says the file is there. (It is not a . file btw.) There are 20 or so files like this according to diff.
Is there any reason a file would not show up in ls -a?