Although a site may have a primary color palette, colors will often look very different in context. Our vision is full of tricks and assumptions that can cause the same color value to look drastically different in different situations. The color in your swatch might look different when used on a different background color, or might not appear as bright when used as a link color, and so on. It's reasonable to expect some variation in the color palette to deal with these issues. Some of these counts seem a bit excessive, though.