"The Trash" is a complex illusion created for your convenience. Sometimes the illusion gets in the way.
Generally speaking, when a files on a drive is "Trashed" its "in the Trash" bit is set the File is NOT copied anywhere, and the filename is added to the list of Files "in the Trash". Finder Trash (as presented to you) is the Union of the Trashes on each drive.
Each drive has its own local set of "in the Trash" files, and the ONE Finder Trash can is a composite of all the Trashes on all the connected drives.
Some files, like System Files, and Time Machine backup files, are STRONGLY protected against deletion.
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to solve your short term problem, just stop fixating on emptying the trash. ERASE your external drive, and all Trashed files on that drive currently "in the Trash" will be erased, so the Trash for that drive, and all the problem files in it, will be Empty when completed.
In the long run, if you are ever temped to change Time Machine files with Finder, DON'T! Those files are strongly protected from being modified or erased, and if you ever could manage to throw some some away, your backup SET would be irreparably damaged, and possibly unusable.