Which tool you used, what message in log you got and are you sure?
I just tried with tool and super tool, both by using repair skill or item on car and in all four cases I lost only 1 of stacked item each time.
im not sure about cars, as i remember i used regular tools like 2 or 3 and it all got disappeared and i got the message "you broke your tools while repairing your car"
i used super toolkit on repairing items, and it also disappeared with the whole stack. it happened with me a lot of times