Not bad bolts, it's just what can happen to the bolts when the giubo goes bad.
The link in #10 shows what can happen if the car is driven too long with a deteriorated giubo. The bolts wiggle and wear, elongating the holes in the output flange.
Your post said "when I got the old guibo out I saw these chippings or whatever you might call it. The bolts holding the guibo were also kind of like this, looking like something had been rubbing on it, or chipping it or something."
Any "chippings" you saw could be from the bad guibo allowing the bolts to wiggle, though I did not notice chippings or damage in your photos.