'Belay' means 'stop'.
Act 4. The ship. You select a destination and the Captain's bark is 'belay that order'. Thing is, belay means to 'make fast' or 'stop, don't do that'. So her saying 'belay that order' in response to your selecting a destination is her countermanding your selection - but you end up going there anyway.
So either its a mistake - someone just wrote something that sounded 'nautical' to a layperson - or its appropriateness is not clear in the context.
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Edit: For those saying she's telling the crew to stop what they're doing - that still doesn't make sense in context. 'Belay that order' is something you say *to immediately stop someone from executing an order *just* given*.
If she is redirecting the crew she would just issue new orders.