Version of InDesign? Operating system version? What font are the numbers in? If they are OpenType, the Numerator attribute may be set. It could happen if you synchronized the book and the Style Source document had that attribute set in a style.
ID 6.0 Windows 8.1 Numbers are Times New Roman Open Type. This is an ongoing (many years) project that uses the same files year after year, with usually minor changes, but I save as new files every year and create a new book every year. We looked at some of the past years, and it was happening infrequently (didn't catch in proofing). But this year, it is rampant.