I have an Ibanez AF95RW with Super 58 Humbuckers, and the bridge volume and tone knobs act in a surprising way. When the pickup selector is all the way on the neck pickups, I would expect the bridge knobs(bottom set) to have no affect. In the opposite case where the bridge pickups are selected, the neck knobs(top set) have no effect, but when the switch is on the neck pickups, the bridge pickup knobs affect the volume and tone every bit as much as the neck pickup knobs. Is this expected behavior?
Looking at the control diagrams for the AF series, nothing says that your controls are supposed to work the way you describe.
Usually a guitar with two humbuckers and 3-way switch will be wired so when a single humbucker is selected, only the volume and tone controls for the selected pickup work. In middle position the volume and tone controls should work in a blend.
Potentiometers in guitars can be wired differently than in a standard electronics wiring, sending the signal to the wiper pin instead of a fixed end. If repair work has been done on the guitar (possibly a pot replacement) and the pot rewired in a different configuration, it is possible that there is signal crossing.
Sometimes guitar tone controls will share a capacitor to save cost, and a mis-wiring or faulty installation can cause signal crossing there.
A hollow body can be tricky to work the electronics on, so unless you feel like studying some wiring diagrams and fishing around inside the instrument, you probably want to take the guitar to a technician or repair shop.