Kinda... you lose the unsigned slot from your pool. Hypothetical to make the math easy.
Let's say you have a 10M pool and you have signed all but a pick whose slot is 1M and plan on signing him to slot but he fails his physical. You are 500K over going in. If he signs, you are 500k over, no draft penalty.
If he does not sign, your bonus pool is 9M, 500K over is 5.6% over and you lose your first rounder next year.