Yes. You choose which scores to submit on the Common App (and on other application platforms, afaik). An admissions officer would see that you took the AP class (from your transcript) but would not see the score, so they would probably assume you withheld your score because you failed the AP test. I wouldn't say anything here is a red flag. AP scores are usually not super impactful in college admissions, no matter how good or bad they are. Your GPA and SAT/ACT scores (if applicable) are far more important.

You don't have to submit AP test scores but it is highly recommended. AP test scores of 4-5 are highly recommended to submit- scores of 3 you should be weary about. 2 or less don't bother submitting. Hope this helps!

Short answer- NONE of them. Long answers- Whether you submit none, 1 or all your APs to a particular school is completely up to your discretion. So if you have a list of 20 schools, in theory, you can take different approaches to submit your AP test score on an a la carte basis. The College Board AP ordering form allows you to send whatever AP test you want to whatever school you want. And the Common App allows you to self-report your AP test scores. Ivy Leagues generally give only college credit or placement options if you get a 5 on your AP test. Brown doesn't give you AP credit. So you might only want to reserve your 4s and 5s for Ivys and Stanford. And I'm pretty sure that Caltech only gives 5s credit on a few limited non-STEM APs as well. UC Schools, depending on the campus may give college credit for an AP with a 3. So I would check the UC AP credit schedule for each of the UC schools you are applying to prior to self-reporting them to that school. If you are considering applying to Ivys and Stanford, keep in mind the sweet spot for APs is somewhere between 9 and 11 these days as more and more applicants have stronger course rigor than in prior years. So plan out your AP course load now, not next year. I recommend most high achieving applicants to take 1-2 sophomore year, 4-5 junior year, and 3-4 senior year. You don't want to wait until senior year to take a bunch o APs because your 10th and 11th grades are most important.