The Check Out feature (a button available on the Booking Data, Edit, and Room tabs of each booking) is only available on a Booking when two events have occurred:
1) the System Date is 'today'. In other words, the check out date is equal to the current System Date.
2) the folio is in balance and no amount is owed or needed to be refunded to the Guest.
Until both of these conditions have been met, the Check Out button will not appear to check out the guest.
If you are having trouble performing Night Audit and getting the System Date to accurately reflect your operations, then call Support for assistance or see: https://support.bookingcenter.com/index.php?/Knowledgebase/Article/View/235 for understanding the difference between Manual and Auto Night Audits. Understanding and working the Night Audit is very important.
If there is a problem with balancing the folio (getting charges and payments to equal 0), then you need to either modify a charge or payment, or get a manager to use a 'Write Off' (or other 'payment type') to balance the folio.