First and foremost there can be bully's in Kindergarten. So yea this little boy could already be bullying your son cause he sees him as a weak link or awkward cause of his autism. My son has Aspergers and is nearly 5. I know he is awkward with children and doesn't behave as the rest of them do... And guess what he already gets ganged up on by THREE boys constantly. He's 5! The teacher always says they are just chasing.. But my son says they are chasing and calling me names. So I asked him what would happen if they caught you. He said I don't know I just keep running so they can't basically. So I talked with the principle and she is handling it. He already got to the point were he didn’t like to go to school.
So considering you don't even know what the story is and your notes you are being provided don't say much. I would most certainly march into that teachers office and very kindly ask her what is going on. She is seeing things and if your son is making things up or leaving things out she can assist you. You can also tell her what your son has said and maybe shed some light on what she doesn't understand so she can watch this all more closely and see how to put an end to it. Best of luck!