Here is my theory: In this example, an Indesign document has two placed PDFs. PDF 1 using Font X and subset to accommodate 125 characters. PDF 2 using same Font X and subset to accommodate 100 characters. Individually the PDFs do not present an issue. However when the Indesign document containing both PDFs is exported, there is a conflict of the font subsetting. Perhaps the subsetting becomes 100 characters, leaving 25 characters unaccounted for, and displaying incorrectly. The complete font download will include all characters regardless if they are used.
I work with publications/magazines where supplied adverts are placed in one ID document. I have encountered this font issue and have resolved it with a complete font embedding. It doesn't happen often, but does occur.
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