Ben tells Juliet that they have activated the implant in Claire, to make her sick, in order for Juliet to "cure" her and earn the trust of the 815 survivors. The implant is inconsistent with the events in season one, in which Alex frees Claire to save her life, telling her she was going to be killed after they performed a C-section and took her baby. There would have been no point in giving her an implant to make her ill in the future if they planned on killing her.
During the flashback to the plane crash Ben's hair changes between the scenes shot at the start of the season and the new shots with Juliet.
After the plane crashes and Ben and Juliet are at Mikhail's, Ben says that Juliet called him a liar yesterday during their conversation following her telling him he has cancer. However when talking to Jack about whether they believe in God, Ben says that he found out he had a tumor on his spine and then two days later a spinal surgeon fell out of the sky.
When Jack, Kate, and Sayid return to camp they come around the bushes one at a time. After Kate emerges Sayid's legs can be seen as he steps forward and waits for his cue to enter.
When Juliet goes over Rachel's chart with Ben to confirm that her sister's cancer has returned, she somehow fails to notice in the upper right hand corner that her sister has apparently switched genders as well. The chart says this information belongs to a 5'11, 187 pound male patient.
Juliet tells Ben that she ordered X-rays on his back to see if his pain was caused by a fracture or a herniated disc. Herniated discs can't be properly diagnosed through X-rays, only MRIs.
When Juliet is injecting Claire with the medicine to save her life, she didn't remove the excess air from the needle.