Okay I looked at your model. It seems the error was a misunderstanding between process flow vs 3D model, regarding which controls the model.
You can do everything in process flow, but the combiner object was already setting the batch size so the process flow batch activity was just messing up your model and leaving a box left behind. Additionally, after the combiner combines an object, it become just 1 flowitem. You also don't need the subflows as it will automatically send the whole pallet to the AGV (because they're all one item) so you can move the Load and Unload straight into your process flow. Your labels were a little bit strange as well in your process flow.
Another issue was you were sending the pallet of items via AGV and also via an 'A' connection from your combiner to the processor which was messing up the AGV system. There were some other weird syntax errors, so just choose things exclusively using the black arrow drop down menu.
Here's the model for reference! I hope that helps.
arquivoforum123 help.fsm