It all depends where the speaker and the listener are in relation to each other. 'Come' indicates a movement TOWARDS the speaker. 'Go' indicates a movement AWAY FROM the speaker. Let's say that you want to enter the doctor's room. You are waiting at the receptionist's desk, outside the room. The receptionist would say 'Go in', because your movement would be away from this speaker. The doctor would say 'Come in', because your movement would be towards this speaker. Simple, isn't it?

Go in: Entra / VE adentro. Come in: Entra / VEN adentro. --> Cuando dices "come in" ordenas al sujeto a entre hacia donde estás tu. Cuandos dices "go in" ordenas al sujeto entrar a un lugar lejano o próximo a ti en el cual obviamente no estás.

"Come in" is something you would say to someone who is outside when you are inside. "Go in" is something you would say if you were outside and you wanted to tell someone they should be inside.

Both have the same meaning.. The main difference is that "come in " is asked in a respective manner and whereas "Go in" is asked in aggressive manner