Had a look at them before, trying to find the stains. At first I thought the reflection was giving white spots in the image. When looking closer, I do indeed see some white spots on a few beads.

These beads are quite a common type of Czech beads, made to resemble garnet. I have not seen stains like this on them before. It is a clear glass, and not very prone to impurities. The molding process does not really make stains like this, not in a clear uniform glass. I can imagine it is some type of damage done by water with a high calcium content (lime scale), but then I would imagine the label and the thread to also be affected by the water. Same goes for any type of mold that could grow under damp conditions.

So basically, I have no idea. Perhaps someone spilled paint on them? Or some type of paint/glaze used on other beads got splattered?