Brown, oh no, it's supposed to turn green!
Just kidding. You have nothing to worry about. The brown coloring is simply the natural chemical reaction between the acid and exposure to air and light. Sometimes freshly mixed Vari-etch will immediately turn brown and other times it will take some weeks for it to occur.
There is nothing wrong with the mixture and the color will not affect its performance in the least. If anything, the change in color will be a good indicator that your Vari-etch isn't just a bucket of water, but is indeed a bucket of acid to be treated with care.