Different style of numbers in endnotes in text

https://community.adobe.com/t5/indesign-discussions/inconsistent-sizing-in-3-digit-superscripted-footnote-numbers/td-p/14954801

It looks like a font-related problem, in which ID is selecting mismatched number forms for... some reason.

I can't think of any specific fix (without having a sample file to dissect), but you might try this:

• Review the assigned Endnote paragraph style for any odd font settings.
• Change the base font for Endnote to any reasonable alternative, to see if the (Opentype?) faults persist.
• Create an entirely new Endnote style, from scratch (based on "No Paragraph Style") and assign it to both the Endnote process (in Endnote Options) and by direct application.
• Create a numbering Character Style and apply it via the Endnote style using a GREP or Line Style.

It seems like one of those should fix the glitch.

Or you can start with the basic "corrupt doc" fix: save the document to IDML, open that file, save it as INDD under a new name. Does the fault persist in that file?