I've just started playing, so I don't know if this is a bug, but I tried to get my bots to collect a tool if their hands are empty.

Ideally, collect a tool and use it until it breaks, then go collect another.

Might just be your script. Try changing it to be similar to the one in the image. 

The general storage is used to store the tools.

I did that, but it just looped through the Repeat section.

However, stopping and starting the bots again reset the loop (although I didn't notice them stopping again).