Adventure games usually work in that way - you can pick up stuff you encounter, put it in your inventory and try to use it whenever you want to. Is this realistic? Probably not. Should this be discuraged? Maybe.
You don't want the player to walk around and pick up random stuff? Fine - then don't give them an inventory at all. Or make it more realistic and let the player only pick up one item in each hand. Or make an inventory with very limited item count. Or... options are endless.
If you don't like the established mechanics, make new ones. But do it for the whole game and don't just use it in one place as an excuse for lazy puzzle design.
You don't want the player to walk around and pick up random stuff? Fine - then don't give them an inventory at all. Or make it more realistic and let the player only pick up one item in each hand. Or make an inventory with very limited item count. Or... options are endless.
If you don't like the established mechanics, make new ones. But do it for the whole game and don't just use it in one place as an excuse for lazy puzzle design.