The only time I have experienced "brown spots" in regard to plastic bags is in throwing some old knit-type tops in them (the clothes were clean, just getting rid of then temporarily - Hah!) and after sitting in the back of a closet for awhile, I opened the bags and noticed that sweat spots or if there were any imbedded grease spots in the items that there were permanent brown spots (couldn't even bleach them out). I also had put them in cheap shopping type plastic bags. Other than that, I have used plastic for years and haven't experienced problems.
Marysewfun