a few possibilities to check,

Are you using the same player at two different positions on defense?
Are you using the same position in two different spots on defense? ie) you can have three DT, but only 1 right DT, 1 left DT, and 1 NT, same goes with other positions except MLB (4 max here) and left/right CB (2 each here).
Are you using any players that are injured?
Are you using any players that you have sold on the transfer list?

Most likely, one of these is what's causing your problem. If there's something else I'm missing, hopefully, someone else will correct me.

Hope this helps.