When the scriptures speaks of "the disciples" or "his disciples," how can we know if the apostles are meant?
The only way to tell is to look at the context of how the word is used and even then that is not a guarantee. Obviously if they are named or if it refers specifically to the twelve, then it is easy to determine. Most people think that Jesus normally is referring to the twelve on most other occasions when he is speaking to them, but there are a couple of anomalies that would need to be explained. For example, when the apostles were choosing a replacement for Judas in Acts 1:15-26, they listed that a minimum qualification had to be that it be someone who had been with Jesus the whole time. Two men were deemed qualified. What were those two men if they were not some type of disciple?
So, in a passage like Matthew 12:49 "Pointing to his disciples, he said, "Here are my mother and my brothers" he could be referring to all those who were following him including the women (hence the reference to "mother") or just metaphorically to the twelve. I see no easy way to prove either position.