Brown stains are often caused by exhausted developer. It can be from developer on the tongs that has been exposed to air too long and then transferred to the print.
If the "stains" match the color/tone of the developed portions of the image, they could be pressure marks from the tongs. Mechanical strain can "expose" the emulsion, that is it can alter the silver halide in such a way as to cause it to be developed as if it have been exposed to light. Excessively heavy pressure from the tongs can cause the areas to develop.