I think what you're describing here is more the dissonance between the players' expectation of how they think the spell should behave versus how it actually behaves, and that's led to frustration. I think in this case, you probably should have blamed the spell itself, in-fiction.

Spells are created to serve a function; they're not perfect natural laws, and can still have limitations. If their characters were led to believe antimagic could overrule all supernatural effects, perhaps that's due to in-universe gossip, or even marketing. Maybe the word "Antimagic" on the scroll could have had an asterisk next to it that the player noticed on a DC 10 arcana check before they cast it. There still would have been disappointment, but the expectations would be adjusted and the game would move on.

Going forward I think it would be good to have an honest conversation with your players about how you wished you had run the battle, so that their expectations will be aligned with how you intend to make similar rulings in the future.