The question "He doesn't like you?" is like the question "Er mag dich nicht?"
The word order in the question "Mag er dich nicht?" is like the English question "Does he not like you?" or "Doesn't he like you?"
It's a subtle difference, but it is a difference in both English and German.
"ihr" and "er" do not sound the same, neither on Duolingo nor in real life. Differences in vowel quality can be quite subtle. If you can't pick up the difference, you need more practice. I also recommend using headphones.
I think this does happen in some exercises (when "er" is in the first position) but not in this one. I can only say that I've noticed a clear difference between the two words in audios from other sites. I'm not entitled to say that this means the audio here is wrong though. And if you pay attention you do get used to it, anyway.
I have been seeing a lot of this negative questions. Are they common in German? Why does Duolingo focus so much on them and not on the positive questions? Is it jsut a fluke of the system or is there any significance to this?
I'm just asking because I find these kinds of sentences, from a learner's perspective, quite awkward to say, both in my head and out loud...
No it shouldn't. "He doesn't like you" implies already known information. As in: She just told you that she asked him out and he said "No, I don't like you." To which you replied "He doesn't like you?" This is a "comprehension question" where you are basically retelling information you already know and are just looking for confirmation.
"Does he not like you?" is an actual question. More specifically, a polar or yes/no question. If (in the above example) she said to you that she had asked him out and he said no, you could then carry on the conversation by asking "Why? Does he not like you?" Which you don't know the answer to. Maybe he said no because he already has a girlfriend or simply that he was busy that day. You don't know the answer.
There is a large difference between the two questions.
Would this sentence be like the English "Doesn't he like you?" or more like "Does he dislike you?" In general, will native German speakers use negatives the same way English speakers do? For example, in this sentence is the speaker more likely to be thinking that "he" likes "you" or that "he" dislikes "you"?
The statement "he likes you" follows the english word order "er mag dich"
Turn that into a question: "does he like you?". In English we use the word "does" in German you put the verb at the front of the sentence "mag er dich?"
Pose the question as a negative "does he not like you?" where to put not/nicht ist not always easy in both languages, but in many many cases you put "nicht" at the end of the sentence. "mag er dich nicht?"