I had a similar problem about six months ago. My beads weren't partially drilled, but the hole on the big end (opposite the hook eye side) had really sharp burrs left on almost all of the beads in a pack of two dozen. In fact, the burrs were sharp enough to cut and fray my thread (6/0 Danville). I smoothed them with a diamond hook file and that seemed to work fine, but beads are a fairly expensive part of a fly and it seems to me you shouldn't have to do this. I don't recall which brand of beads they were, so I won't guess.
-Darryl
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"If we carry purism to it's logical conclusion, to do it right you'd have to live naked in a cave, hit your trout on the head with rocks, and eat them raw. But, so as not to violate another essential element of the fly-fishing tradition, the rocks would have to be quarried in England and cost $300 each."
~John Gierach
My one wish is that when I die my wife doesn't sell my fishing stuff for what I told her I paid for it...