Riddles are often a play on words so here's my guess -
"In the first bowl there are 3 out of 5 Poisonous Apples." That means that there are a total of 5 Poisonous Apples. It does NOT mean that there are 3 Poisonous Apples and 2 Regular Apples in Bowl 1. It means that there are 3 Poisonous Apples in Bowl 1 and 2 Poisonous Apples in Bowl 2.
I believe Bowl 1 has 3 Poisonous apples and nothing else. Bowl 2 has 2 Poisonous apples and nothing else, meaning you can't even eat 3 apples because there are only 2 apples in the bowl.
Eat from Bowl 2 because you won't have to eat any apples, especially after Bowl 1 eater is poisoned.