Bind a back with its pages without stains
Most likely, the stains appear because the glue diffuses into the paper - the paper being porous, or the glue too strong / dissolving. Try a different paper / glue combination.
About the wrinkles: I guess that you make the binding manually - as in using the bare hands, without any kind of presses, clamps, etc. Use the proper tools, practice using those tools until you understand all their secrets, and then go ahead doing the beautiful work.