Please provide additional information about your situation. What version of InDesign and what operating system are you using? Have you recently updated either your vesrion of InDesign or operating system? How have you been going about exporting your pdfs? Have you been using File>Export>Adobe PDF (Interactive or Print)—the best way? Or have you been trying to create pdfs using your printers option to "Save as PDF"—not a very good way at all. Has this been happening with all files or just specific ones? What are the makeup of the files as far as number and type of imported graphics, page count, etc.? Please be specific.
Did you have any warnings other than this when the file was packaging? You could try to just export the pdf under file/Adobe PDF presets choose pdf quality you need and see if you get any warnings that are more clear? Sometimes a font could cause it too?