OK. You're doing some sort of processing, and you're getting a contaminant that's really screwing up your process. That much is clear. Of all the possible sources of a blue fiber that has a solvent extractable dye, I don't think there's a definitive source for us to determine. But process controls are up to you.
Start simply: sweep up your area, air it out, run the air flow in the area, check and clean air filters, and anything you can think of. If you think you've done enough, do it again, and see if it reduces the occurrences, and realize -- that means you aren't doing enough, and do more.
Consider doing your processing under air flow, or in a containment hood or glove box.
Control your environment: have your workers brush their uniforms before they start work, and try to track the source.
Consider dry runs with just water. Then filter the water. Now you'll have captured the fibers, and can have them analyzed.