Some bikes have metal (steel) pipes in the coolant system and while they are plated they still rust slowly..
I think the kawasaki is bad for this (that i can remember) - there is one by the water pump, and the yamaha r6 too that i can speak of.
So it's common for water to come out a little brown depending on the state of corrosion of that pipe , i wouldn't worry one bit.
One way around it is to get one of those silicone hose kits, i think some of them have custom molded silicone pieces that replace the metal junctions.