How many chunks is your level made of? If it's any more than 10, say, and you're only picking from a set of 50, then the chances are more than likely that you'll have the same chunk twice. Randomness != Uniqueness. And, assuming that each loot is chosen with equal independent probability, the outcome of having two of the same loot is mathematically exactly as probable as any other outcome.
All computers can only ever generate *pseudo*-random numbers, it's true, but they're more than sufficient for any gaming applications. If you believe that your code is less random than it ought to be then please post your code - you might have a faulty implementation.
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