Depending on how this is done, there are a selection of soloutions. If you mean people are submitting bogus scores to your high score table or such, that's an easier one to fix, just make each flash game provide a secret key passed over POST to the score script which will only accept scores containing that code. Or even better, encrypt the scores in the flash game and send as an encrypted string you can decrypt at the other end, so sending the score script large number won't affect it.
The other possibility i can think of is people using a RAM hack to actually change the numbers in your flash game on their computer. To my knoweldge there is nothing you can do about this.