I think I might understand this a little. It rather depends on the relationship between Alice and Bob: a general solution won't exist. You've only given one example, which is a problem, but let's run with it:
Alice: ..... Charlie .... Dave .... and then he --
Bob (interrupting): By 'he' you mean Charlie or Dave? You mentioned both.
This is, to be clear, absolutely not Bob's only option. Alice is saying that asking this way (including explaining why Bob doesn't know) feels like an attack, like Bob is saying "you talk wrong" and I can kind of see her point.
Things Bob could do instead:
- Wait until it's Bob's turn to talk. Perhaps it will be clear by then who "he" is -- some side mention of his brother or his wife or whatever will make everything clear and there will never be any need to ask.
- If it's not clear, at the next natural point, take a guess and present it as such. "He Charlie?" Alice can agree, just really nod, and keep right on going, or say "No, Dave" and keep right on going. No explanation of why Bob needs to confirm this information or how Alice miscommunicated on the "he" front.
- If Bob has misguessed and is corrected by Alice, and feels now that he is being told he's listening wrong, he could say "I was unsure, because you mentioned both." This depends on their relationship: how often they converse, who is the "senior" in their friendship or relationship, whether this pattern recurs elsewhere in their lives.
I talk a lot with someone who often can't find the word they want and just dump all the work onto me, without noticing.
So I want you to look at -- you know the thing? that we put on the thing? -- it needs to be adjusted and we could, I don't know, kind of, you know, check it and -- I don't have time today so is that something you can do?
Seriously. Since we talk a lot and this happens a lot, I will say "the thing that we put on the thing? that doesn't narrow it down much" or "you haven't given me any information." I am clearly saying "you're talking wrong." I wouldn't do that with someone I only talk to once a month, or with my aged mother, or someone much younger than me. I would instead ask clarifying questions. "What thing? Where do we put it?" without mentioning that they said something ridiculous as a first pass.
So for Bob and Alice, if they are adult-child-and-parent, or two neighbours who occasionally chat over the fence, or coworkers, or a married couple -- it makes a big difference. In most cases I would suggest sticking to short clarifying questions that do not explain the ambiguity or "go meta" about whether something was obvious or not. Stay focused on the conversation Bob and Alice are trying to have. In some cases, especially if Bob is starting to feel "now I'm the stupid one" or if Alice is snapping at Bob "try to keep up!" or "why do you ask me that sort of thing of course I mean Dave" then it may be appropriate to explain why Bob felt there was an ambiguity (not quite the same as insisting there is an ambiguity and trying to explain it.)
I do find that going over conversations afterwards and saying "you called me stupid" "no I didn't" "well you rolled your eyes and you also said 'I can't believe these questions' so that's the same" "no it's not you're just reading things into perfectly harmless comments" "no I'm not" and so on do not improve anything. They lead to at least one person claiming "I have to walk on eggshells around you I'm constantly afraid you're going to misinterpret what I say" or "it's exhausting to talk to you because you're very vague and ambiguous and expect me to figure out everything myself while you don't bother putting any thought into your sentences" but they don't actually reduce ambiguity or get people's conversational needs met.
In fact, the concept of communication needs or conversational needs is a very useful one here. If the purpose of the conversation is to exchange facts, the needs of the people are very different than if the purpose is to team-build, to create a plan together, to reassure, to comfort, or to persuade. I might suggest to Bob that discussing communication needs should happen at a higher level. Not "I need you to agree that saying 'he' after mentioning two different men (or boys) was ambiguous and I was right to be unsure who you meant" but "when we chat over breakfast I like to feel that you care whether or not I can follow your story" or "if we are going to plan this project and get it done, I need to be confident that we're referring to the same things when we say 'he' or 'soon' or 'agreed'." Talk about emotions and feelings and confidence, comfort, assurance, and support. Not about parts of speech or sentence length.