If there is an ambiguity, there is an ambiguity. But there are few verbs which can form the passé composé with both auxiliaries (they need to be in the restricted set which is able to take être as auxiliary and have also a transitive form), currently we (with the help of Stéphane) have three: monter, descendre and sortir. And I’m hard-pressed to come up with a situation where there is a true ambiguity, context usually gives lots of information about what is plausible, as timing relationship and as meaning.

You could say that je suis descendu is ambiguous, but as soon as there is a context, it will be clear that firemen are carrying you down the stairs (and the idiomatic way to say it would be something like on est en train de me descendre instead of je suis descendu, French uses the passive far less often than English) or that you went in the basement to fetch something.