There are a million things that can be off.

For pixel art, you want to use the pencil tool instead of the brush, as the latter emulates a real brush and therefore generally blends the pixels over the brush tip area for less precise but more natural result. The pencil, on the other hand, will set pixels precisely where you want but offers no smoothing.

The blending mode of the tool as well as that of the layer will determine the apparent color of your pencil strokes. The "normal" blend mode uses the actual colors of the layer so generally this is your choice for pixel art.

Both the drawing tools and the layers have an opacity setting which will affect the apparent color. Also, some tools have a "flow" setting which is like opacity but will accumulate over time for an airbrush-style control.

There can be adjustment layers above the layer on which you draw, affecting the apparent color of your artwork. Fortunately, it is easy to hide the layers above if this is the case.