Domenicos comment lead to the following idea (I am posting this as an answer, as it is too long for a comment):
Let CAT denote the category of small categories and CAT′ denote the category, whose objects are small categories except for the fact that the composition needn't be defined on the whole of Mor(A,B)timesMor(B,C) (but just on a subset of it). Associativity and so on should hold, whenever it is defined.
Then there is a obvious inclusion Functor CATrightarrowCAT′. One should check, whether it has a left adjoint L:CAT′rightarrowCAT. Then one can make out of the data above a object in CAT' by adding an additional isomorphism from X to Y and one doesn't have to worry aboutthe compositions of that iso with the morphisms in CAT. Using L one could make a honest category out of this.
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