The only explanation I can think of is that Duo would still be using a dictionary of synonyms which has made the system suggest "cheque" instead of "check". Of course, this "cheque" is nowhere in the course that we (volunteers) have written.
I would have to agree with you. Customs agents do not "control" baggage -- they inspect it or check it. I suspect that EN "control" was put there by someone to make it easy (not) for learners. In fact, it is not correct.