You should add if statement like for example...

|---------repeat forever

||----repeat until hands full

||find nearest stone

||move to stone

||pick up stone

||----

|

||----repeat until hands empty

||move to stone storage

||add to stone storage

||----

|

||----if stone storage full

||move to incinerator

||add to incinerator 

_______________________ 

I think your suggestion that the game include "if" statements is good.  In your example "if stone store full", "move to incinerator", "add to incinerator", you could replace the first line with "Repeat until Stone Storage not full" and you would get the same result.