Bounties give coins only when you deal with the whole wave of enemies. Also Bounties won't give coins for the wave if there are enemies from the previous waves.
Can you share a video recording?

I don't know how to record on my phone, but I think I know more.
It looks like when a new wave comes before the current one is defeated, you get Bounty; then when you defeat the earlier wave, you get the Bounty again. Then when you defeat the latter wave, you don't get the Bounty.
I play with waves auto calling when the previous is defeated, and on 4x speed. I haven't tried other configurations yet

For me, an easy way to reproduce it:

• Open level 5.1, build a Bounty (anywhere should work, but I've been putting it on the Damage V tile at the end). Don't build any other tower.
• Start the game on 4x speed
  Once the timer runs out, the next wave starts, and you get your Bounty bonus. Once the two enemies reach your tower, you get the bonus again.