Like most of these conundrums, this "paradox" is just a trick of language.
The only sense in which "one of them is a girl" means "at least one of them is a girl" is a strictly mathematical, logical one, and the sense in which "what's the probability both of them are girls" gives an answer of 1/3 is again a strictly mathematical construction which means "out of a randomized trial consisting of selecting between the scenarios where at least one child of mine is a girl with equal probability, what is the expected frequency of the scenario where my children are both girls?".
Nobody really talks like that in real life, hence when you hear it first, your brain automatically assumes the mother means your second meaning when she really means the first. When you say "one of them", you're usually thinking of a specific one, such as "the eldest one" or "the one playing in the garden". But using the strictly logical sense as above, the answer differs.
Your follow-up question asks, "why does the order matter?"
We say that each child has a 50% probability of being a boy or a girl. In order to identify which child "each" child is to calculated the combined probabilities, we need to give them separating labels, which we apply an order to for convenience. Child A being male and Child B being female is a different case from Child A being female and Child B being male, even if they're both cases of "one boy and one girl".