I take a weapon from my backpack, I can’t pick it up

Do you have any plugin installed that tries to clean up entities? If so, that plugin is the cause, not backpacks. It just happens to not work very well with backpacks because of the way backpacks uses containers. The entity cleaner plugin can be updated to work better with backpacks by using its API to know whether a given container belongs to a backpack or not, so that the cleaner plugin can ignore backpack containers.