Hello, and thanks for the question.
As you stated, the first sentence implies that the call lasted half an hour. The sentence itself is poorly constructed because it contains three consecutive prepositional phrases--"on the phone", "within the half hour", and "with me"-- but it could be taken to mean, "During our half hour phone conversation, I mentioned this." The second sentence implies that a topic was mentioned within the past thirty minutes during a phone conversation (regardless of the total time of the call). A way to reconstruct the sentence to make this meaning even clearer would be to state, "I mentioned this within the past thirty minutes, during our phone conversation."
Hope this helps!