Silly

This is our first winter with the spa and we actually forgot to check the water level until it was below the highest jets. We shut the spa off and after a few days were able to drain, clean and refill the spa. We now notice bubbles coming out of a few bottom jets that never happened before and that the spa noise is louder (coming from water fall turn on knob). If I turn on the waterfall the noise decreases. Do I have a problem I don't know about? Thanks Silly