I zeroed in on this same error message today. I can't tell you exactly what was causing it, but I can tell you exactly the object that was causing the issue. It was a 1-row, 2 column table. In one cell was some text that included hyphenation ("in-process"). In another cell was a drop-down menu with only two options defined: pass and fail.
I noticed that as I was scrolling through the document, as long as this particular table was visible, I would get the same "bad hyphenation" message continuously, line after line, and once the screen threw up 8 lines of this same message at once. But once I deleted the object, the error no longer appeared, and when I re-created the same table sans hyphen, no error messages.
I must note that once the error message appeared, when I tried to work with the table-cells, the object no longer functioned as a joined table but instead worked like individual fields.
My suggestion is to go through your document and look for table cells with hyphenated text, delete them completely and then re-type them without the hyphen included, and see if that takes care of the problem. That's how I got rid of my error.
