I must be really lucky. The only time I have ever had contamination problems was when I used my fingers instead of gloves to move prints. The source of the contamination was very obvious: streaks running down the paper from the corner I had lifted the prints. Went to stainless steel tongs, no more contamination.
I use the same trays, tongs and graduates for lith printing that I do for normal printing. But I always rinse my trays out and let air dry between sessions. As I said, I must be very lucky!