Previously I had a problem to delete a directory which was unable to be deleted, and I tried many workarounds to sort the problems out but It did not work.
It happened because you didn’t have the proper permissions for it;
directory /run/media/user/usb_name/.Trash-1000
Anything in /run/* is not persistent and shouldn’t be relied on. It might be back later. Especially after a reboot and something that seems to be created by another OS;
Using sudo to delete something is like using an angle grinder to fish out a stubborn splinter from your finger. Sure, it might work, but heck the chance of amputating your finger, or even your hand is so great, it’s really not worth it;
This might seem over-the-top, but trust me, in the long run it’s worth it, read up on permissions, that will help you not use an angle grinder when all that’s needed is a nail file.
I almost think @Aragorn has something on permissions, if, and only if he wants to chime in.