Using version 5.17.6 (build 10516) on Windows Server 2016. I have this behaviour in the UI Explorer style interface and when downloading files using the -delete option. Not all files are deleted, just a small number of them. The files are downloaded properly and when the delete process is invoked, most of the time the system says that the file is in use and cannot be deleted. I've logged using the UI when invoking Download and Delete (F6).
I can repeat the process over and over and slowly I'll be able to delete all of the files.
Edit: It seems like if there was a short delay between the operations that this would work around the issue. If I download/delete the items one-by-one everything works fine.