What do you mean by "spotting" exactly?
If you're afraid it's mold soak it with 1-2 tbs of baking soda in just enough hot water to cover all the parts. It's a natural anti-fungal agent. Remove from the water when cool enough to touch then take a toothbrush and brush everything off (it may be helpful to add a little extra baking soda to the toothbrush for extra scrubbing power). After that, if you want, then soak it in vinegar and hot water. Hit it with the toothbrush again. If it's still not gone to your satisfaction, you can soak all the NON PLASTIC parts in a mild bleach solution. Rinse that well and then hit with the toothbrush again. I doubt there will be anything left alive on the parts after the baking soda and vinegar.
If it's hard water spots/scaling soak all the pieces in a lot of lemon juice, a citric acid & water mix, or a descaling agent. Those spots are completely harmless, but removing them may improve your coffee.
You're prooooooooooooobably being overly cautious. There's not much for mold/mildew to eat on coffee equipment unless it sat wet and covered for a long time.