Sometimes when creating joints like finger joints (also known as box joints), dovetails, lap joints, and the like, you will end up with small gaps in the joint. You can use wood filler to fill those gaps, but I think there is a better solution.

When you are cutting the joints, set aside some of the sawdust that results from the cuts. When you are done, take the sawdust and add some woodworking glue. Work the glue into the sawdust such that you end up with a paste-like mixture. You want it as dry as possible, but still sticking together.

Take that mixture and work it into the joints. Use a fine tool (I like to use a dental tool) to work the mixture deep into the joint and fill the gap completely. Once the glue has dried, sand it down and you are ready to stain.

The glue in the mixture will affect how the wood takes up the stain, but since these joints usually have end grain exposed, the difference is not usually noticable.