Small area of muddy watercolor
If your watercolor painting is largely made up of clean watercolor washes but maybe 5% is overworked and muddy looking I often just let it go as it will not alter the overall look of your painting. This is not a hard and fast rule however. Sometimes a little muddy area can add additional textural interest to your painting.
Large area of muddy watercolor
Depending on how large an area is muddy it could unfortunately fit under the category of not repairable and would be repainted after analyzing when so much of the painting ended up overworked and muddy looking. At worst you can always paint over it with other mediums e.g. pastel or acrylics.
Composition doesn’t look right
First try to ascertain what is wrong with your composition. See if it can be corrected with tonal glazes or the addition of darker objects to break up a space into a more interesting one, etc, etc.
However if it is just not possible to correct the overall composition of your watercolor painting then you could try cropping the painting into a smaller shape.
Using various mats that are smaller than your painting pass it over your artwork in both landscape and portrait formats to see if there is a successful smaller painting within the not so successful larger one. One of my students regularly did this when she was still developing her watercolor skills and often ended up by selling the cropped watercolor.
A large section isn’t right but the rest of the painting works just fine
Washing out the offending section under the tap using a sponge and repainting can certainly work here. I have had a couple of paintings to which I have done this with very good effect.