Questions while reading

I was reviewing a story to review when I realized that, like any good reader, I was asking questions about the text. What I realized during this story is that there is a difference between questions that engage the reader, and questions that throw the reader out of the story, reminding them that they are, in fact, reading a story.
In SpecFic, what I write, it is important to remember that the average SpecFic reader is intelligent and engaged in the work, so they ask questions about the text while they read it. In SpecFic, a question like "what the hell is going on" is okay as long as there is enough content to give the question shape. Questions like "is this the person that was mentioned a few paragraphs ago but wasn't introduced?" tend to throw the reader out of the story.
Hopefully I can find greater clarification between the two types of questions. It may be different because I am a writer myself, and I have developed an "editor's voice" while reading, trying to find the function of a paragraph in the greater story. Instead of just enjoying the story, I edit and critique. This is a flaw of workshopping. Even when I read Analog or F&SF or Asimov's, I get the editorial commentary while I read.