While hiding in the woods, Ellie gives her Machine Gun to Anatole as she sets off in pursuit of John. However in the next shot she is holding it while moving. In the following shot its gone again.
As John and Ellie prepare to swim across the flooded area to the chateau, they remove their shoes. John makes a point of telling Ellie they are to the to leave no trace. In the next scene they are wearing their shoes.