I think i have an idea on what happened to Vegapunk and Bonney while they were in the flashback/dream sequence. Caribou has always been known to get crazy information through eavesdropping. What if while Caribou was on his way to kidnap Vegapunk or Bonney, he accidentally stumbled into Kuma's memory as well and gathered some information that he could use to benefit himself. It would explain their disappearances.