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There are 2 possibilities. The first is more obvious: the area where this teleport led has been flooded.
The second is rarer: the generator created 1 teleport. I had this happen to me on Diamond. There were 2 teleports on the native spawn, along a dirt road, just for decoration.
In general, a non-functional teleport in the starting zone or in areas adjacent to it is a reason to send the save file to a judge to check for a bug that requires a restart. Because there is a risk of playing for 2-3 weeks and then finding out that there is no way to reach the opponent at all.