Quoted from LyonsRonnie1:
Go back and watch again. I just rewatched it. He tested the red dye and said "we're getting 9.689" then the guy said 'That'll be our base reference for fully saturated" then the other guy said "about 9.7". The other guy says "Anything that's 1 or above will be a positive indicator of the actual dye"
So they check the muddy water, and it says "11.98"
Then they redo it when Rick is there, and get 19.47. They remark that even though they can't see the dye, there's some concentration.
I re-watched it. You are correct, I was remembering the numbers wrong. However...
The initial sample wasn't pure red dye. It was a sample of water with the dye in it from the source bore hole. It seems unusual that it would be higher after going through the flood tunnel, but they are pumping pressure into the bore hole. It certainly isn't redder on the other end, but maybe that pressure is making a chemical found in the dye more concentrated when it comes out on the other end.