"Why are you making a face like that?" "Why are you looking at me like that?" "Are you mad at me?" These are the correct way to ask all three. "Why are you looking at me like that?" and "Are you mad at me?" are both very natural expressions heard all the time in English.

what Chris says is true it is the standard English and used globally, by Americans, Brits, Kiwis (New Zealanders), Australians and all the global English speaking countries. They are the best ones to learn and remember. Keep the other suggestions in your vocabulary so that you can vary your responses, and become more natural. Able to respond better to how you interpret the facial expressions of others.

You could also say, "You look upset. Is everything okay?" or simply, "What's wrong?"

You could also say, "You look upset. Is everything okay?" or simply, "What's wrong?"

Also “what’s with the face?” (For very informal /family situations). “What’s wrong” “are you okay?” “Is everything alright” ? Are more common