Possibly a bug when using companions that can act as workbenches like Veronica. It seems items are not returned from the inventory to the managed containers properly when using the "pull from containers" feature.
Repro steps:
Make footlocker in Novac hotel room a managed container, put crafting materials that are used in workbench recipes in it
Talk to Veronica -> "Could you help me craft something?"
Notice you are able to use the materials in the container for crafting as expected
Don't craft anything, exit the menu
Leave dialogue, crafting materials are now in your inventory instead of the container
Using the workbenches added by Home and Safehouse Tweaks in the same room works as expected so it seems to only be an issue with companions.
Repro steps:
Using the workbenches added by Home and Safehouse Tweaks in the same room works as expected so it seems to only be an issue with companions.