If I may take a stab at interpreting this exchange, she likely got mad because (in her mind) you couldn't possibly understand how she feels due to the inequity in parenting time. You have him more often, so (in her mind) you aren't experiencing the same sense of loss as she. Then, by telling her that it's tough on all of you, she probably felt guilty and defensive at being reminded she caused this situation, and also that you diminished her feelings by chiming in about yours. Just my guess.
Perhaps saying "Yes, that would be upsetting" or "I can see how that would be hard for you" would have been better?
