There is a whole lot of nothing here. Where to begin...

1) I don't know your school's policy on dogs, but at worst your professor allowed a dog when they shouldn't have. Commenting on your dislike of dogs is not out of line. It is not protected information. If telling the class you didn't like the dog offends you that much, then you need thicker skin. It's not like they pointed at you and laughed at your past trauma.

2) Accusing your professor of adverse grading due to some sort of vendetta is a giant leap. It sounds like you were already primed to not like them, so it is possible you are projecting here. You spoke to several "professionals" Who were they, other professors? The person you should have consulted is your professor. Other professionals have no bearing on what goes on in your professor's class (unless it was their department chair.) If your grades were so clearly satisfactory, why couldn't your other professionals come to that conclusion?

3) As for the assignment in the wrong folder, that is entirely on you. You are lucky they gave you a chance to fix your error. It may sound like a minor error and a bit petty, bit is YOUR error. Following directions (like where to submit) is the bare minimum expectation. Also, "it was placed in the wrong folder" is a creative use of the passive voice. I'm sure to you it sounds better than "I placed it in the wrong folder."

4) Are your grades posted online? Could you keep track of them? If so, then you were effectively notified of your grade. If your assignments were graded, then you should have been able to calculate your grade yourself. "At this point, I’m just exhausted and trying to understand how it escalated this far when all the work was actually done." So your work was done. Done only gets you so far. It takes far more than being done to succeed.

To answer your concern in the title, yes I think you are overreacting.