One key point here is that bounty chips do not "transfer". This has two possible meanings. First, when a player is busted out of the tournament, they must give up their bounty chip. This is the bounty chip that they purchased at buy-in, or their most recent rebuy. However, they do not give up any bounty chips that they have won (they don't transfer any bounty chips to the hitman except for the single bounty chip that the busted player purchased). Second, there are two ways to keep your bounty chip. One is if you win the tournament. The other is if you are busted out by a player who has not purchased a bounty chip and you have the "restrict bounties" option enabled. When you bust-out of the tournament and keep your bounty, that's it for that bounty chip, you keep it forever. It does not "transfer" to your next rebuy. If the player wants to rebuy and also have a bounty chip, the player has to buy it at the rebuy.
The other key point is that your players did not purchase any bounty chips at their rebuys, and you have the "restrict bounties" option enabled. So the winner of the tournament kept his/her rebuy, and two other players were busted out of the tournament (their first bust-out) by players who had rebought, and so the hitmen in those situations did not get to collect the bounty chips. Thus, 3 people "kept" their bounty chips.
Correcting this is going to depend on how you play your bounty chips. If a player wins the bounty chip of a player they bust out regardless of whether the hitman in this situation is on their initial buy-in or has rebought, then just uncheck "restrict bounties". If a busted player gets to keep their bounty chip and continue using it by rebuying (i.e., their hitman doesn't get it if the player decides to rebuy, which by the way would suck in my opinion), then you will have to correct this by editing the buy-in of the rebuying player to remove the bounty chip, and then edit the rebuy of the rebuying player and add the bounty chip.
Hope this makes sense. Limited time today so I'm typing as fast as my fingers will go.