It's a very hard topic called "Declination of masculine nouns in Genitive case with endings -а and -у" :D
I hate it, it's sometimes not intuitive.
I'd say "без лимона" when you think of it as an object with specific "borders" (like countable) and "без лимону" if I think of it as a material without a fixed shape (like uncountable)
But it might be that only one is correct. In that case I'd vote for "а" because it's a clearly outlined object...