I defeated my 3rd Mighty Kraken located at Spoiler R20 and then my ship finished its journey one more square to Spoiler S20 . Afterwards when I went to collect my winnings from the Mighty Kraken it showed I had 4 pirates left. After I tapped the checkmark to continue it showed a prompt screen to go to a pirate stronghold that held approximately 140,000 gold and 160,000 grog. I know I wouldn't win any fight with 4 buccaneers so I left. Now it is nowhere to be found. Was this a glitch or a secret?
The strongholds have a fight button above them just like the 4 fight ports. Perhaps you tapped on the fight button by mistake after the Kraken screen? We don't remove the button though so I am not sure why you couldn't find it again
Maybe, but I'm certain I didn't tap anything other than the green check mark for the battle with the Mighty Kraken. Is there a stronghold close by that I'm not seeing? In that region I don't have any that are undefeated.