There is no fix besides the right length spoke. If you know someone with a Phil machine the spokes can be cut and threaded, otherwise it's buy new.
BTW- generally same brand spoke and nipple combinations allow for the spoke to go 2mm or so beyond the top of the nipple. Rounding up would only be 1-1.5mm and shouldn't have been a problem. I suggest you revisit your spoke length calculation, and check to see why you came up so long.
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