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Fundamentally smoke interferes with the pheromone (smell) communication 'language' that the bees use to raise the 'We're under attack' alarm.
In addition, when smoke enters a hive, bees immediately divert to eat* as much honey as possible as there is immediate danger from fire, something bees seem to be instinctively aware of. So they start preparations to abandon the hive at a moment’s notice. This diverts them whilst the beekeeper takes their home apart.
*Not actually 'eat' but store the honey/nectar in their honey stomach that they can regurgitate from later.