Consider the following text:

Superscript[¹](#notes)

Blah...

...

#notes

 - This is an anchor.

The ¹ character in the text above is Unicode Superscript One (U+00B9).

If you save this as an UTF8 file using latest version of Notepad++ on the latest version of Windows 10, then close and reopen the file it will be detected as Thai TIS-620 character set and ¹ character will be garbled:

It seems that the presence of non-alpha character (i.e. symbols or digits) immediately before ¹ is triggering the problem.