Even just before 2 pm every weekday makes it difficult to schedule a full load of classes. I guess maybe they play a very condensed schedule after spring break? There is literally almost no way that you could have a full load only from 9-10 and 12:30-2, so all the players must be dealing with this.
My advice is to take a deep breath. At most schools, schedules can shift quite a bit even in the first week of classes. So classes that are full may open up again - he needs to find out how this works at his school, by talking to upperclassmen. I realize it's difficult now that they are on break, but surely they are snapchatting or group texting. Does he have a residential advisor who is not a baseball player that he could ask?
I know from my son's school's parent Facebook page, a lot of parents worry about this, when the answer is that the student has to learn from other students how things work.