My own classic mistake has always been remembering (and reminding players) that consequences can be resisted on social rolls, not just combat and sneakery.
Maybe not so much a mistake as a stumbling block to watch out for and find a personal preference for is stress and harm balancing. The rules make it optional as to whether resisting harm avoids all of it or just bumps it down a category. It can seem too soft a touch to say that you can always just choose not to take any damage, but the harm and healing rules are pretty harsh. It can be tempting to see the resistance roll as akin to an action, in that a poor one might let more harm through, but that is a mistake as the greater stress taken is already the result of that bad roll, and worse harm as well is double punishment. Accounting for quality, tier and scale, and being transparent about what can and can’t happen as a result of a roll, take some time to get the hang of, but are important things to learn to keep a game consistent and fair.