If you using photoshop when you should do that:
1) check if unchecked Image->Mode->Indexed Color;
2) open Image->Mode->Color Table... dialog;
3) double click on one of duplicate colors, write down in notepad or wherever color number (# symbol) like 3333ff or just copy it in buffer;
4) double click on second of duplicate color, it's number is different, replace it with number from previous step - this will change second color to same color previous was;
5) when you done with all of duplicates check Image->Mode->RGB Color and then switch back to Image->Mode->Indexed Color. After that you may look at Color Table and see that dupes removed.
Maybe this was too detailed, but whatever. There's other way, maybe more simple one - try filling color that have dupes with Paint Bucket Tool with other color (non present in your sprite to avoid mess) you'll see unfilled pixels, fill them too and then fill 'em back to needed color.
Veterans Day