My son who is 10 weeks old twitches what could cause this?

My son is ten weeks old and has been sick with a really bad cough and congested, i took him to the doctor and he put him on a breathing treatment,he has been on it for about two weeks, he started getting them every four hours, and now he only gets one before he goes to bed. He still is congested, and has a minor cough, but now he twitches. his feet and eyelids. he doesn't seem like he is in pain but what could cause this,and is it something that should be taken up with the doctor or am i over reacting?