Attach a piece of sandpaper to the sander that is two grits higher than the last grit you used to sand the floor. For example, if you last sanded the floor with 180-grit sandpaper, you'll need to at least use a grit that is 220.
Sand the area of the floor that has the uneven stain on it. Wipe off the dust from sanding with a tack cloth.
Mix 10 parts water to 1 part white glue in a small container, and mix well with a tongue depressor. Dip a foam brush in the mixture and coat the blotchy stained area with this substance. Allow it to dry for four hours.
Sand again with the sandpaper you used in step 1. Wipe away the dust from sanding with a tack cloth. Dip your 3-inch nylon brush in your stain color and coat the uneven area. Allow it to soak for 20 minutes and wipe the excess away. Repeat, if necessary, to get the color even.
Seal the fixed area with the sealer you used for the rest of the floor and a paint roller. Allow it to dry overnight.