Endnote citations inserted after superscript/subscript incorrectly follow the format

Hey everyone, just after help for what seems like a simple issue that I can’t seem to resolve after spending heaps of time on Google.

I’m inserting citations into an enormous document that includes the use of subscript and superscript throughout, with some citations placed after subscript and superscript usage (i.e chemical compounds). The problem is these citations follow the format of the sub/super script they’re inserted after, it’s trivial to fix them manually but given the size of the document not realistic to do so every time I update it.

Is there a way to stop this happening using the output style editor or something? Included a picture for reference. Thanks.