Weird noise the first couple times I press the brake pedal
 

So I slid in some ice a couple months ago and went up on to a curb. The dealership that repaired it replaced the brake lines because they were scratched up. When I first tried to pick up my car I didn't make out of the parking lot because the brake pedal was making a really weird noise, felt spongy and the brakes only worked at about half their normal power.
So I left it and they said they flushed and bled the brakes again. When I picked it up the second time the noise from the pedal was not really noticeable and the brakes seemed to work fine.
That was about a month ago and my brakes still feel fine but I have noticed the first couple times I press the brake pedal down I hear a weird noise (which the deal said was the rubber squeaking on my shoe). I listened in the engine bay and you can hear it even more loudly in there. It sounds like it's coming from the master cylinder. It sounds like air rushing through liquid when you press it down.
After you press it down a few times you can't hear it anymore, or at least it is much quieter.
This may be completely unrelated but I have noticed it's harder to shift gears (especially when not moving). It feels like my clutch isn't disengaging completely or something. I tried adjusting the clutch pedal and it seemed to make it easier when you first start driving but it gets worse as time goes on.

Now both pedals are making a weird squeaky noise that gets worse the longer the car is driven, especially in stop and go traffic. Could air be getting into the car because the brake lines weren't replaced properly?

If the pressure on your brake pedal feels spongy, there's air bubbles in your lines or fluid leaking out of your system. The squeaking noise you hear, is it more like an unlubed door hinge noise or like a scratching noise?

The clutch uses the same system as the brakes, maybe you got air in the clutch line?