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For one group, I could never plan out a boss encounter simply because they would change course at the drop of a hat. I don't mean "let's use diplomacy instead of war", but rather "let's leave and do something else". My fault because I enabled them, but I'm glad to not have that responsibility anymore. Fortunately, their habits taught me to plan for the worst. For a normal group, I keep a backup build or a completely hidden villain tucked away for emergencies.
Let's say that the group decides to eliminate a thieves' guild and succeed in completely scouting out the membership. They think they know what to expect. They outfit themselves perfectly. The combat gets under way and the group manages to quickly work through their opponents. The "boss" fight is over in a few rounds and they're feeling godlike. Then that fat little messenger boy runs in scolding the group and otherwise acting very unlike a street urchin. It turns out that the messenger boy houses a tsochar warpriest/magus/other-kind-of-caster-fighter-hybrid and things really heat up. Make sure that the "red herrings" can double as "omg we should have seen this coming" if needed.
You may end up not using the contingency plan, but that means you can refit it for a future campaign.