I don't know anything about the vaccine/autism link, but I can say with absolute certainty that there are some obscure side effects to certain vaccines that nobody seems to know about and when asked about them, everyone seems to "know nothing".
Case in point:
When I met my wife, she was a 30-something single mom/OT student. She was working on her degree and at the time had no medical insurance (pre-Obamacare). She was required to get an MMR shot due to her having to work (for free) at Kindred Hospital in Greensboro. Since she had no money, she had to go to the Health Department for this shot to be administered. Within hours of the shot, one side of her face began to droop and she was diagnosed with Bels Palsy. Worst part of this was that it happened just prior to our engagement pictures. Some of her patients actually thought she was making fun of them since the day before her face was "normal" and now was distorted.
She had never had any signs or symptoms prior or since. Fast forward a couple years to her working at a different hospital and having to get tested for the MMR titer again. They tell her that she has to get another MMR shot because it wasn't registering. Magically, even though she can provide the exact date of the MMR shot at the Health Department, there is no record of her getting the shot, the follow-up visits to determine that she had Bels Palsy nor any record of the doctor or clinician she saw either time there. Twilight Zone kinda stuff. She was finally exempted from the MMR shot after much struggle.