There is no reason to think so. Barwise and Moss were perfectly aware
that
1) The foundation axiom is not "for all a, a is not a member of a",
but the stronger, purely set-theoretical statement "for every non-empty set b,
there is an x in b such that the intersection of b and x is empty",
2) the foundation axiom is perfectly compatible with impredicative
comprehension axioms. In particular, the impredicative axiom for the
existence of sets of natural numbers that I stated is fully compatible
with the foundation axiom, as is clear from the fact that it involves
only numbers and sets of numbers.