It could also be someone salvaged them out of some surplus gear without knowing they shouldn't cut the fiber. You can reterminate them, or use them as is with a cleaved end but you might not want to use them at full rated output, unless polished, even then, they will no longer have a anti-reflective coating which to me, means don't run them at full output, I don't want to suggest how much percent is OK to run them at in this case, but for myself I would not worry at 75%, if properly cleaved. I guess I just suggested, didn't I. Other members will probably have their angle to add.
I have a lot of those 50 watt FAP's, it's a lottery whether you get a good one, one with some dark fibers, or bad. On ebay, if they represented it as used but fully functional, even if in the listing they say no returns, you can probably return it anyway.