Can't pick up any stones.

I'm not sure how to ask this but is there a glitch in the system where if I reach 999 on the score that I am no longer able to pick up anymore stones/rupees? I am asking for my cousin. If you need anymore information about the game please ask. But I am new to this and so is he. He is on the level where he is trying to defeat the "Skeleton King"(?). Again I have no idea what I'm talking about so bear with me please.

sounds like you've gone up to maximum cash so untill you spend some rupees then you cant pick up any more, are you after the medallions for the old man right now cos i can't remember any skeleton king near the start the only 3 bosses i know of there are the team of blue knights one which turns to red when you eliminate the others the 2 sandworms and the giant worm thing whose tails you have to hit in order to harm it