Visual Bug when Digging

I've ran into the same issue and although I can't get the exact procedure of how to force it to happen I have noticed a few repeat actions that lead up to this. For me usually the game has been running for more than an hour and more often than not its usually right after the Duplicant has eaten then going directly to dig or procure water within six tiles of where they've eaten. Other things I've noticed is that if the colony itself has been expanded to nearly seven times its starting size. More than likely its a graphical glitch due to the immediate cache file being overloaded and the first items, such as Duplicant tools, are forgotten by the game.