For some reason the rule is treating a single new line at the end of the file as multiple lines and creating an error for it.
@chapel, thanks for contributing! Can you provide your config and a sample file showing this issue? I'm not able to immediately reproduce and this would help me debug.
I continue to not be able to repro this. If you have two \n at the end of your file, that is an error. 1 is ok though.
Closing this for now until OP responds with a repeatable test case.