It won't cause any structural problems. But it can have a problem on fit of other parts. In other words, you shift one piece then you may have to shift the next piece, and the next, and then you might have a problem.
If you cut a piece too short. It's best just to put it in your scrap pile and cut a new piece. Balsa is fairly cheap.
You can go to a craft store and buy balsa, just to have laying around, if you are planning on building more models. You'll need it, if you are going to fly your model.
If the piece is a factory die-cut part and it's the wrong dimension.... which rarely happens...*cough-cough*
then you can use the template on your plans to make another part. A good habit is to check the dimension of your part against the template on the plans before you pin it to the plan.