This game is 6 years old now. Commentary here is really for any other developers who happen to read this. Play around a bit and notice the button controls. They're a little bit confusing, right? You can learn the pattern of entering and exiting the menus, but it doesn't feel intuitive.
The issue seems to be how 'using' a workbench to get the workbench menu ends up swapping the subconcious mnemonic of 'button that opens menu is the same button to get me out of the menu' that happens with inventory use.
Notice how the inventory is also able to be displayed in the workbench. Pressing inventory next to a workbench to take you to the workbench menu instead would be a better fit.
What would happen if you pressed the 'use' button next to the workbench? Perhaps automatically revert to 'pickup tool' and pick the workbench up (to be placed down again with another 'use' keypress)? This is a seperate issue from the menu one, but this too could result in better gameplay.