Henry shagged Mary before Anne. This means his relationship with Anne counts as incest under church law at the time. However, you could get dispensations for most things.
Re. the witch thing - imo, people did believe in witches, but rather the way we might believe in, say, cold war spies. We know there's a few real ones out there, but we also suspect, mythologize, and quite enjoy the idea of them. And sometimes we're pretty sure people are getting framed when they're not guilty.
In the period I work on (which is a little earlier but not much), there's a conflicting attitude towards physical 'proofs' of witchcraft: you could as easily see Anne's 6th finger, or a deformed baby, as evidence of a person to be pitied and cared for, as evidence of witchcraft. In fact, sometimes deformity (in adults, generally), is associated with power: the idea that someone is marked by God in their suffering.
So - whew, I am long winded - basically I'm saying they pinned it on her and people would have known they were pinning it on her.