I had this problem with my bass because it has some sweet spots on the neck, if that's what you're talking about. The long term fix is to take it to a guy who know to have a set up. I had to replace the neck and now it's much smoother, though I lost the Fender logo on the process. Whatever. Another natural way of dealing with it is to change the song to a key that doesn't use the offending fret (in my bass is sometimes the low G).
Then you have compression an eq, which are the artificial way. Compression is cool, it helps even the notes and also can give you a specific tone, like the compression you get by using Ampegs. With eq, you have to dial by ear until you find the offending note.
Then you have your playing technique, if that's the problem. If a note is too loud try to pluck it closer to the bridge.
Finally, if you're miking then maybe it's your room the cause of trouble (standing waves). Get far away from the corners and walls, maybe that'll help.
Cheers, Andrés