there are two situations that i can remember at the moment where you can abuse to earn extra bounty with bounty mods:

• selling all mods on the end of the wave (more money stored = more bounty)

• putting the bounty mod when the last enemy of the wave is about to die and there is no space far from tower (the last mob won't give money, but the bounty from the mod is usually way bigger)

for the first you can or make mods cheaper to sell on the end of a wave, so the player will lose money if he wants to keep doing this, or you can make the money counts only in the next wave

for the second you can just make the bounty based on the % of the time that the bounty mod was present on that specific wave, so if it is bought at the end of it the mod will give almost no income for the wave