a properly seamed patch should be virtually invisible and a lasting item. you did pay for a whole install(i assume-sometimes it not possible to get a whole floor in w/o a seam: therefore seam kits and men with skill and experience as i have found out recently) and it could be an easily negotiated item. certain glues used under the material could cause a stain as you described or a reaction to something on the slab with the glue. since i`m a "just learning" at this point, i`ll sit back and listen in. good luck.