I have recently upgraded a couple of 300D Firewalls to FortiOS 5.6.3 and in doing so upgraded the FortiAP firmware to 5.6.3 as well (for 221C AP's).
Found an issue with the AP's not upgrading from WiFi Controller GUI after FortiOS was upgraded to 5.6.3.
1) If I went into the AP list and edit an AP and try and do the upgrade from within that window (in GUI) it was not compatible and fails.
2) If I select the AP from the list and Right Click on the AP in the List and choose to Upgrade - then it works ok (selecting a pre-downloaded FortiAP 5.6.3 (build 493) firmware image locally).
Use the 2nd option as a workaround.
Have logged with Fortinet - and being looked at - but might be a while off.