This gel can be recovered in most cases by fully destaining in methanol:water: acetic acid, followed by a fresh round of staining.  In severe cases, the deposits may be removed by gently spraying the gel surface with alcohol. 

Blotches can be caused by overhandling of the gel, or by handling the gel without gloves.  This can create uneven surfaces or protein deposits that can bind Coomassie to the gel.  To minimize this problem, handle the gel as little as possible, and always with clean gloves – have us prepare a gallon of ready-made 10X Tris-Glycine-SDS Buffer for you!

Occasionally blotches result from using a dye solution that is not completely dissolved-  The dye crystals deposit on the gel surface and produce an area of the intense background.  This will eventually disappear during destaining.