It could also be any other of the composition errors (substituted fonts, as mentioned above, subs. glyphs, H&J Violations, etc.)...
If it's not built as a character style, and not one of the above mentioned comp errors, then it might have been achieved via a script or plugin...but it would probably still show in the char/para palettes.
Can you send me the file? Sometimes what trips people up is that there is a Rule Above with a check box, then a Rule Below with a check box and one or the other gets missed.
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