What kind of guitar? String trees? How's the string height at that particular slot? It could be a few things, but if everything's in order otherwise, the slot may just need to be worked/smoothed out a little.
MIM Tele with trees on 1 and 2 only. Aftermarket bone nut. I really can't go any lower with the cut, wondering if I just start smoothing it out with a deeper angle towards the headstock.