The bruising and blood stains on Claire's neck when she's speaking to Samuel the last time change between shots. As a regenerator she should not have bruises to begin with.
When Peter is talking to Sylar about books, there is a big number 4 on a green background painted on a wall on Peter's right. The shot then changes to Sylar's perspective, and when it's back to Peter's perspective, the background of the number on the wall is blue.
In the first season it showed when Bennet joined the company and first met Thomson and his invisible partner Claude. However, this shows Bennet joining the company again, but this time his boss Thomson is much younger than when we last saw when Bennet joined.
Claire's bullet wound, received in "The Art of Deception", isn't healed. It should have healed instantly.