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In Banjo-Kazooie, Bee Swarms with Beehives are first encountered in Gruntilda's Lair in the room outside Freezeezy Peak, and in Gobi's Valley. As long as they have a hive, they are harmless, and will only attack if their hive is destroyed. Bee Swarms without a Beehive can also be found in Click Clock Wood in summer, and will attack without provocation. Hostile Bee Swarms can only be defeated with Wonderwing, requiring prolonged use of it, as the attack only picks them off one at a time.
Banjo-Kazooie: Grunty's Revenge
In Banjo-Kazooie: Grunty's Revenge, Bee Swarms are found in Spiller's Harbor and Freezing Furnace, inside Grunty Industries and are always hostile, regardless of whether or not they have a Beehive. They can be instantly defeated with Wonderwing.