Most likely you have food residue that is now growing mold and mildew. Try putting 1/4 cup borax in the bottom of the dishwasher and then running it through a cycle. Also using white vinegar in place of a rinsing agent (ie jet dry) will help keep your dishwasher clean and keep spots off your glass.
Unfortunately if it's really bad you will have to scrub it well with a toothbrush and a baking soda paste to get all the gunk out. Don't use any harsh chemical cleaners in your dishwasher, besides putting harmful chemicals on your dishes (many are not water soluble and do NOT wash off) they can damage the rubber gaskets and cause leaks.
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