If you have gotten a couple of bad grades in middle school would it decrease your chances into getting into prestigious schools like Yale ?
No, middle school doesn’t matter
Even if they were HS courses taken in MS, it is highly unlikely that a college will care.
I would encourage you to try to learn from your middle school years. Time management, study skills, study groups, and be honest about whether you are doing your best effort. It is okay to ask for help, and now is a great time to make changes and improvements.
Also look at your overall activities and interests. Middle school is a great time to explore possibilities, but as you enter high school, you want to be narrowing down your interests to the ones you are most passionate about.
Your middle school grades can’t be viewed by colleges unless the middle school class was one that your high school accepts credit from. With that being said, try not to repeat your mistakes. 
No, but you have to ask yourself why you got bad grades.
People who go to Yale, etc. are very smart and very hard working. THey are intellectually curious and do beyond the minimum.
So why did you get bad grades? Didn’t study? Don’t care about grades? Have trouble understanding the subject? Didn’t do homework or read? Put in minimal effort?
So figure out what the issue was and rectify it…change your study habits and work hard. If you don’t understand something, ask. If you do poorly on a test. talk to the teacher until you can understand the topic.
No.
Though bad grades in MS are probably a marker that the student is not destined for extremely selective schools.
Colleges don’t see middle school grades so from that standpoint you are fine. But 1) most people cannot flip a switch and turn from a mediocre middle school student into an outstanding high school student 2) if you are not tracked into the higher level HS classes based on your performance in middle school that could be an issue.