sunflower and peashooter problem

hi i had the same problem but i think I've came to a solution.
at first, I bound the 2nd ability to the 'c' key on my keyboard, and from that point I've noticed the same issue you described.

so anyways' i played around with the controls and key binds and after resetting all key binds (2nd ability is now on the '2' key) the issue wasn't bothering me anymore and i could use the 2nd ability on both the pea shooter and the sunflower, I hope it'll help.

since i have 2 extra buttons on the side on my mouse I've bound my abilities (1st and 3rd) to them, and the 2nd ability to the mouse wheel button, and it seems to work that way without cancelling the ability immediately, you can try the same if you can.