I'm helping my brother fix the electric service to his garage. We successfully ran a line from the house to the garage. The old one was torn up due to tree roots in the yard. Anyway that part is done. Once inside the garage at the junction box there were 6 different lines inside the box. One each for the two lights, one each for the three plugin outlets, and one for the garage door opener. Is that common? Shouldn't the lights and outlets be joined into separate junction boxes so that fewer wires go into the junction box for the lead wire from the house? I tried to join all of the wires (a total of 7 of each including the one from the house) together and managed to do that but whenever we switch the lights on or off the breaker flips.

You could add another Jbox and split the circuits. Cramming them all in the same box could be a violation depending on the size of the Jbox. What typically happens is that a neutral or switch loop leg gets into the power side. 20 amp? UF feed wire? Sounds like you got a wire crossed.