I think it would have to be quite a strong dye to show up in the line, and how much would it discolour your body tissue I wonder?
As for the bubbles, I always thought they were a big no-no. Then whilst an in-patient for an unexplained runaway BG increase one time, I queried a 4 inch long bit of empty line when the nurse was changing my water infusion bag, and she said it's not enough to worry about.
So...I guess bubbles only present a BG control problem by causing interruptions to ones basal flow, but I always purge the line of any air which is the full diameter of the bore, but don't bother about the tiny specs of air. Never had any bubble related problems in 6 years of pumping.