C.C.
My daughter is almost 5, and she is one of those kids who will say that she doesn't want to sit near someone. The thing is, she isn't doing it to be mean (at this age, they have very little concept of how they are going to be perceived by others). She does it because she is easily overwhelmed and tends to need quite a bit of personal space in order to feel comfortable. There are some kids who get really huggy with her or are loud and she just can't handle that. She used to shove kids away from her, and we have encouraged her to use words to solve problems. She's doing that, but then other kids get their feelings hurt because she says she doesn't want to play with them or whatever.
If you'll notice, his little friend seems to have this issue at times when she might be having a hard time dealing - when she's hungry (before she eats lunch), when she may be feeling overwhelmed (on the bus, or at the end of a play date).
I would just let your son know that his friend is trying to use her words to express what she needs from him, and he needs to listen, and give her some space when she needs it. Maybe schedule your play dates to be shorter so they can be more successful, and maybe have them right after the kids have eaten so they both have a good level of blood sugar going. In other words, set them up for success!