Comparing a couple of text files whose unique difference is a CR-LF at the end of the last line I get "identical".
What matters is "ignore linebreak styles". If it's unchecked then the difference appears.
Honestly, I'm not sure I can really call it a bug.
But if you say "Ignore linebreak styles: CRLF (DOS/Windows) vs. LF (Unix) vs. CR (Mac)" I expect EDP ignores if it's a CR, LF or CR-LF, not if in a file is present and in the other it's missing.