Hi Kalonde! It's more likely that you are hearing "Il en a" rather than "Y en a". They sound similar to our non-french ears when spoken fast, so it get us puzzled sometimes!
The sentence you hear is "Il y en a" = there are some.
This would indeed be the only case where both are present in the same sentence, but only because "y" is part of the fixed expression "il y a" (there is/are).
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