Yes I had raised that as a bug & will be fixed in an upcoming version.
You can still upgrade the AP by doing it from the list.Managed FortiAP's
-> Select AP to Upgrade , Right Click on the highlighted AP and select
Upgrade Firmware.Then Upload File a...
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...
