When copying a directory to a different location where the destination directory already exists and you would simply use:
cp -R source-dir existing-dest-dir
then you are actually putting a copy of source-dir inside existing-dest-dir instead of replacing existing-dest-dir by source-dir.
The solution to this is to use a trailing slash for source-dir:
cp -R source-dir/ existing-dest-dir
Watch out since, e.g., zsh removes this slash on <tab>.