After doing some research, the following conclusion was made. To solve this problem, we need to rewrite the whole mathematic engine of island generation. It will take a huge amount of time. We can work on other bugs and improvements or on this single issue. Actually the problem isn't so big. In average, there's 1 island with such problem among 100 normal ones (of course, this depends on your luck).
Explore is totally random from the beginning until the end, and sometimes this random isn't so favourable. Please consider this a Critical Miss.
Sorry for the inconvenience.