Cherrymon mentions during its story that Digimon have been losing their memories for around eighty years (by their count). Given Analogueman is the one behind this, that means for eighty years he's had free rein to do whatever he wanted to the Digimon of File Island.
Furthermore, think of the Digimon who are wandering the island, attacking one another. How many Digimon have died in all that time? And given there's no sign of Primary Village, where are they going?
File City is called "Beginning Village" in the Japanese version, making it the place where dead Digimon respawn. This is why there's fresh and in-training Digimon fluttering around, and why does your Digimon's digitama make its way into Jijimon's house once it fades away or gets otherwise killed. The amount of babies on the village, though, is something to think about for a second.
At the Misty Trees, if you venture far enough, you will find a particular area with stone statues of Digimon. Going there early enough in the morning will trigger an encounter with a Kokatorimon who, if you beat, will join the city. Since they contribute a statue to the city when they join, you would be led to believe that those statues are just their sculptures. However, their city statue is in a completely different style than the ones in the forest (read: it's of poor quality), which puts Kokatorimon's craftsmanship into question. Then you realize Kokatorimon are based on cockatrices, and their Petra Fire attack does transform their targets into stone. You could get to the conclusion that Kokatorimon didn't actually make those scultpures themselves, but are the petrified corpses of Digimon that just happened to pass by their nest. Worse yet, you can clearly visualize a Biyomon, a child Digimon, amongst the casualties.
