It really depends what the noise actually sounds like and how loud it is. If the lens was not mounted properly then there is likely to be a gap between it and the camera body which would allow dust in. If dust gets behind (and into) then lens then it might be causing the noise?
Also depending on what lens it is, maybe you have switched on the stabilization feature? This has a motor which makes (at least on my Nikkor) a much lounder sound than the focusing motor. When I got my first camera I didn't notice this sound at first until I started listening to the noises, that is why I'm making you aware of it.
Ultimately I doubt the lens was damaged from being improperly mounted in such a way that it would start making a noise that would get louder over time. Considering you are new to the camera my guess is that it is another aspect which you have not yet familiarized yourself with yet,