I've put extra pumpkin puree into ramekins at little baked pumpkin puddings. The recipe I use calls for the internal temperature to come to 175 degrees. Any higher and you apparently get curdling. With the ramekins being so much smaller, they get to the target temperature much sooner.

I imagine that the small pie molds will have the same issue, so you will probably need to reduce the baking time.

You can also cook some of the moisture out of the pumpkin puree before mixing the custard, which would probably allow you to add less thickener. Just cook it in a sauce pan over medium-low heat, stirring often, until it's more like a thick paste. You can drain the excess moisture, but it takes longer and you lose flavour.

The challenge in putting a standard pumpkin pie filling into a pocket pie mold arises from the typical "weeping", i.e., release of excess liquid from the filling, which then makes the crust soggy. This can happen with any custard pie; it results from over baking the custard itself. To avoid this, an attentive cook will blind bake the bottom crust before adding the filling, to allow for a shorter cooking time, and then will take care to avoid overcooking the pie. You can't do that, obviously, with a pocket pie, so you need to counteract it in some other way. The easiest way would be to add a starch-based thickener to absorb the excess liquid, such as corn starch or a modified food starch thickener (such as a product called "Clear Jel," which is sold under a variety of brand names and can be ordered online). I don't know what recipe you are using, but I would suggest that for a standard 9" pie using canned pumpkin puree and the Libby recipe, you mix 2 tablespoons of corn starch with the sugar, stirring well to get out any lumps, before adding the sugar to the other ingredients. Good luck!!

I'm answering my own question but I could. I put all of the condensed milk in the batter and I should have only put half. I thickened the batter with about 6 tablespoons of flour. I put about 3 tablespoons of pumpkin into the mold. They are good!