Soooo much easier in NL, people are just doing it wrong.
When you see the beehive fall out of the tree, run away so you can't see the bees onscreen.
As soon as the bees are offscreen, don't use the D-Pad to equip the net. Open your inventory, and equip the net this way. The bees can't move while the inventory is opening, closing, or open, while the D-Pad switch lets them move.
Once you have your net equipped, immediately face the direction bees are coming from. When you see the bees onscreen, press A. You just caught your bee!