Puff pastry can be a bit tricky but I really admire your ambition to make it from scratch. From the description, it sounds like the issue is with the water content of the apples and not your dough because your puff pastry came out as desired when baked on its own. Here are a few tips and suggestions that may help solve your problem:
1) Not all apple varieties bake or cook in the same manner and specific apple varieties were often originally bred for a specific purpose such as eating raw, baking, or making hard cider. So picking the an apple variety that bakes well could help with this problem. Here's a few links with some suggestions and explanations for several common apple varieties and how they fare when baked:
2) Pre-cooking the apples, no matter the variety, will help reduce the moisture content of the apples significantly and thus the apples in the filling (allow them to cool to at least room temperature so they don't melt the butter layers in your puff pastry) will not weep very much, if any, additional moisture. Here's a link with an apple pie recipe with a pre-cooked filling:
3) Puff pastry is always a bit tricky to bake because of the complexity of what is happening while it is baking. Puff pastry is mechanically leavened, meaning the puffiness comes from steam released from the dough, primarily the layers of butter, so it is important to start puff pastry at a high temperature to convert the water released by the butter to steam so it inflates the pastry and separates the layers and you get the desired golden-brown color on the outside. However, depending on the thickness of the dough and the amount of filling, keeping the puff pastry at that temperature for the entire duration could lead to a burned exterior before the interior finishes. To counteract this problem, you could start the puff pastry at a high temperature, around 400 degrees F, until the dough is the desired color and flakiness, and then drop the temperature to 325-350 degrees F, to bake the interior all the way through to the desired doneness without scorching the outside. Of course, this will depend on many factors so these are only rough guidelines and some experimentation will be needed. I hope this helps!