Capture Net reads:
Equipped character has"Activate->Return target stunned character to its owner's hand. Put a bounty counter on a card you control named Bounty Hunt."

Bounty Hunt reads:
Ongoing:Whenever a character an opponent controls leaves play, put a bounty counter on Bounty Hunt.

So am I safe to assume that when I activate Capture Net and target a stunned character that Bounty Hunt will recieve 2 counters.One from Capture Net and one from Bounty Hunts ongoing ability?

You got it.