As suggested, you should always restart your device after playing for the day , right before bed time. In the morning, your games will open up fresh so you should see your bonus pop up.
If you do not restart and jump right in your game to play, when your game loads up (after you have been away) it takes a few seconds for your game to sync with the servers.
That is why if you jump right in, before your game syncs up, your pops will pop up while you are playing.
Also along these same lines, you may get the coins, but miss seeing the pop up because you were not fully synced up with the servers.
If you feel you are not getting the bonus coins, you can send an email to
support@teamlava.com so they can check your game.