Quite recently I've opened and retreated the similar bug#28791, trying
to trash directories recursively. I did not use a custom
trash-directory, but I got the same error. Turns out that it was
delete-by-moving-to-trash that provoked the error (with an indentical
message to yours). Emptying the ~/.local/share/Trash/ folder solved the
issue for me. I observed that in ~/.local/share/Trash/info/ some
.trashinfo files were created with the name of the directory (say
<dirname>) I was trying to delete, one <dirname>.trashinfo and many
<dirname><random bits>.trashinfo.
That is still a bug in Emacs, at least because the error message is not helpful. It is also in a non-standard format with incorrect capitalizations in-between and doesn't even generate a backtrace by default.
Also this issue did not happen on emacs 25.x.