I have experienced this when both copying files from a server to my computer, and copying files between directories. The subdirectory folders themselves copy over, as well as folders within them, but "loose" files within the subdirectories do not copy. The result is an intact tree structure of empty folders.
There are times when files do copy, in alphabetical order, but once a subfolder is reached, files that come after it alphabetically are not copied. The aforementioned subfolder is also empty.
I searched for someone experiencing the same problem, and came across this old ticket which describes the exact problem I'm having but says it was closed and fixed years ago in #1125.
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