Sometimes it happens. You click on Apply while you have all APs spent. After small pause, you realize that your toon has some spare APs to spend. This is bug. Some enhancements was not applied despite on what the windows shows. Reopen the enhancements window and you will see, what was not applied. Then you can reassign the the spare points again. Don't spend the spare points without reopening the window.
I guess this is probably network issue - lost packets. Enhancements are sent to the server in batches. Apparently, when packet with batch is lost, client doesn't repeat the request.