APs should always be connected to access layer switches. Anything in "user land" connects to them, and they in turn, have uplinks to one or more distribution layer switches, where the "magic" of VLANs, QoS, and such happens.
Core layer switches are where everything ultimately aggregate to. You don't want users, APs, or the like to be directly connected to them, just routers and other core layer switches.
for a more detailed explanation.
But what will happen should an AP be connected to a core switch ? What's the negative effects?
Because then the APs will have to talk to their controllers at the lower layers (access or distribution), and you don't want that unnecessary traffic occurring in the core layer switches. Like I said, Core switches should connect to other core switches and routers. Anything "userland" really needs to be placed at the lower layers, or you are just generating unnecessary traffic for the core switches.
It's just a bad idea. Keep APs, VLANs, QoS, and the like limited to access and distribution layers only. Besides, you really want to have everything connecting to the core switches to use routed interfaces. Even VLANs shouldn't span up to the core switches. All you'll be accomplishing is adding extra load on the core switches, and you want those to be the fastest switches on the network. Sure, you can get wireless distribution controller line cards for CAT 6500 switches, but I wouldn't use them. I'd use high speed interfaces, and maybe VPN, Firewall, redundant supervisors, and traffic monitoring line cards instead.
Again, check out Cisco's recommended campus/enterprise model, and you'll see why they suggest using the Access and Distribution switches for those tasks.