In a small mixing bowl, stir together cream cheese, sugar, and vanilla and set aside.
In a large mixing bowl, whisk together pumpkin, egg, brown sugar, milk, honey, vegetable oil, cinnamon, and vanilla. Add baking powder, baking soda, salt, and flour and stir just until combined.
Spray inside of silicone molds and lids generously with non stick cooking spray.
Add half of pumpkin batter to molds, then top with cream cheese mixture. Top with remaining pumpkin batter. Use a toothpick or skewer to swirl batter and filling.
Top silicone molds with silicone lids and stack on trivet. Add 1 cup of water to Instant Pot, then lower trivet into Instant Pot. Lock lid into place and set Pressure Release Valve to sealing.
Cook in Instant Pot on High Pressure for 10 minutes, then let Natural Pressure Release for additional 10 minutes.
Release additional pressure and remove Pumpkin Bites by lifting trivet out of Instant Pot. Turn pumpkin bites out onto plate for serving.
If you do not have pressure cooker safe lids for molds, cover tightly with foil instead.