Careful with the water there: depending on the stain/staining process they used you can remove the stain when flushing it.
What you experience is, upon the whole, normal. That's why we're s'posed to clean the pipes after each smoke: hold it upside down and tap the rim on a chunk of cork; then take off the stem and use a pipe cleaner to clean the bore, following it by cleaning the bore of the stummel; then bend the pipe cleaner and use it to wipe the bowl; then use the spoon on the Czech tool to remove all the tobacco/dottle/ash stuck to the chamber's walls; then spit inside the pipe and use a paper towel to scrub the inside of the bowl—repeat until the towel comes out clean; then wrap a corner of the paper towel around the pick of the Czech tool and carefully clean/ream the opening of the bore at the bottom of the chamber; then, finally, put the pipe back together and set it on the stand to air for a while.
It's not at all unlike cleaning a gun after you've been to the range.