There could be two reasons for this.
1) When an option is assigned or exercised, the cost basis is not automatically updated to reflect the assignment/exercise price.
2) When do an ACAT transfer, the cost basis does not automatically come over in all cases.
If either of these cases occurs, simply submit a request through the Settings page of your account. To get there, click the gear-shaped button at the top of the page and then click the link on the left side of the screen to open a support ticket.