All children experience insecurities at night and may sometimes have bad dreams. This may be especially true in a child who has had the recent changes in his life that your girlfriend's son has had -- a new adult moving in, moving to a new city, and starting school. It is certainly appropriate at those times to reassure the child that adults are close by and that the child is safe and secure. As soon as the child is comforted he can be returned to his own bed.
This boy's behavior is entirely normal since he has been allowed to do this all of his life. The most obvious possible negative effect would be his coming into your bed at an inappropriate time, and some experts question the impact that sleeping with parents can have on children as they get older and are more sexually aware. You and your girlfriend need to come to an agreement about this behavior. If your decision is to expect her son to sleep in his own bed from now on, you will need to stick to that consistently.