There are rare cases where the use of can creates genuine ambiguity. When can can in theory mean either 'be able to' or 'be allowed to' (as in What if she asks me what he can do?), in practice the context usually makes it clear which is meant.
There is always the option of using may instead, but remember that even in questions it sounds quite formal: May I come in? In positive and negative sentences its natural habitat is official pronouncements: Persons under 16 may not use this facility.
However, may is more often the cause of real ambiguity than can: does They may not go until Thursday mean that they are not allowed to go, or that it is possible that they will not go?