Sorry you had problems with the finishing of your floor. The stain will raise the grain (any loose fibers left from the sanding process). The poly will also raise the grain because the wood fibers will expand like a sponge when the finish penetrates into a tiny splinter that is still attached to the surface from the sanding process and it will puff up as it expands. This ought to be cut clean with the surface with either steel wool, imitation steel wool which could be polyester with grit embedded in the fibers, or fine sandpaper. Then vacuumed up or tacked off. The surface will become smooth after the polishing, but will get a little rough until the surface is sealed. The poly-urethane will seal the surface, or a second coat of stain. This is the mechanics of finishing a sanded surface. The coarser the sandpaper used will result in more grain raise. Once the surface is smooth and sealed, more coats of finish will result in a uniform smooth finish. Because of the two coats of water-based finish being applied before the surface was smooth enough it will take extra work to get the surface smooth. The finisher may need to screen and apply two more coats of finish to cover screen marks and deliver a smooth surface, since water=-based finishes do not become as thick for each coat because of the water content, along with the other solvents.. A smooth surface is what you paid for. It will be easier to clean and maintain. Incidentally if a rougher finish was desired there are special non-slip finishes for special areas, like stair steps, for safety.
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