These problems are caused by the gvfs backend (or thunar), which trashes
files to top-level trash directories .trash-xxx, but lists only certain
of them. It is not particularly related to removable media. E.g. trash
folders of partition mounted under /media/my_partition will be listed in
thunars trash. If you mount it under /mnt, it will not show up.
There are related reports to this issue:
https://bugzilla.xfce.org/show_bug.cgi?id=7813
https://bugzilla.gnome.org/show_bug.cgi?id=604015
#682439 is probably a duplicate.
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