Several possibilities. First, if the pie crust was rolled too thick, then the pie crust doesn't have time to cook all the way through. Similarly, if the crust isn't cooked long enough, then there isn't enough time for the water content in the pie crust to fully evaporate and the pastry will be soft instead of flaky. Another possibility is that your pie filling is too watery. Pie crust can hold up to a lot, but if your filling is too watery, then the water won't all be able to evaporate in the oven and some will be left sitting in the bottom of your pie, to then be absorbed by your crust.