What I do, is make sure my net is the only tool I'm holding so when I shake a tree and they fall I can immediately equip it and run far enough away so it gives me time to turn around and press A when they are near.
Signature-------------- Emotions will never be obsolete
What I've found that works best for me is when it drops, run NORTH. Open your pockets and drag the net to your person, when you do this, it automatically turns you around. Close the window. And the second that you see the bees on your screen, press A.