No I haven't experienced that. I have explored on land mostly, but I have only built a couple of colonies since there is no population growth. I have fought hostile tribes and traded with them without any problems.
I played long enough to advance the game by a year and a half, but I couldn't think of anything else to do. The wood, fruit, and fish were going negative so I only explored as long as the supplies lasted.
Most of my time with the game has been from the same save which was after returning from Palos with more colonists and the Hidalgo title. I kept building storage towers, farms, and houses until I ran out of food. I could probably do more trading and finance food that way to keep the game going for a while if I time the trips to Palos right.