That could be a classic Finder problem where Finder doesn't always update to show you files that it didn't copy itself. Similarly, it sometimes doesn't "hide" things that it didn't know were there.
It's hard to work around this kind of bug, but you can always "prod" the finder into refreshing by restarting it -- to do so, Cmd-Option-Click on the Finder icon in the dock and choose "relaunch". That should refresh anything that's a bit behind the times.
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--Dave Nanian
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