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The fan, hob and cooker are covered by the cooker switch in the kitchen, but the fan is outside of the cooker circuit breaker in the fuse box.

Let me se if I've understood this correctly. Are you saying that turning off the cooker switch on the wall shuts off the hob, oven, and the fan, but if you turn off the cooker circuit-breaker the fan still runs?

If so, then you definitely have some crossed wiring. It sounds as though the fan is getting its "live" feed from another circuit, but its neutral is wired back through the cooker panel. I expect you'll find that turning off some other circuit breaker stops the fan from working.

This really needs to be sorted out, as apart from causing nuisance tripping there is a safety aspect in that crossed circuits can result in someone turning off an isolation switch and the circuit not being dead.