Looks like you got some great answers here! Just want to add that in my experience, I don't hear "is an" very much because "is" used in this way is often combined with the word that comes before it to make "~'s", so the difference between the words "(something/it)'s an" and "isn't" is easier to hear! And generally, when I do here "~ is an" used, the "is" in the sentence has emphasis, so it really sounds like "~ IS an". When said more distinctly like that, "is an" and "isn't" sound less similar.
Also, if someone says it unclearly, I just ask "is or isn't?" People will say things a bit unclearly sometimes, so it's okay to ask! Many native speakers have to ask to hear something repeated, or ask for clarification, because English can be like that sometimes haha