I had the same problem until I figured out a little trick. Its best to start out with a clean unstained hose or one that you took the time to clean with a pipe-cleaner and a long wire to feed through the hose, something I used to do but got sick and tired of looking at it and cleaning it. That is when I suddenly had a slight revaluation on how to prevent the problem to start with, here's how:
After finished using a nice clean unstained hose to do a water change, make sure your hot water side on your faucet is hot at least 110F but no hotter then 120F. Then before sucking all the water out of your hose to put it away, place the end of the hose in the bathtub and run hot water through it just enough that it reaches the end pushing all the tank water out and cooking all the bacteria. The shut off the hot water and turn the python in reverse with cold water to suck out all the hot water. DO NOT run cold water through the hose before storing and repeat at the end of water change. You'll never have a discolored or germ funky hose again. I do it to all my garden hoses I use on my aquarium as well.