I'll start & everyone can post what they catch.
1. Not thinking plots through with an eye toward potential mass viewer displeasure.
2. Writers forgetting what they wrote & plots falling flat as a result.
3. Relates to #2: Sonny gave up all rights to Michael & Morgan. So, why did Carly need his signature on the permission form for Michael's surgery? Also, Edward & Monica are clearly the only people in town who don't know about Sonny giving up his parental rights or they wouldn't be threatening to sue him for custody of Michael.
4. During Michael's surgery, a nurse questioned a decision Patrick made in a routine part of the operation. Nurses don't question a doctor's decision unless the patient's life is at risk.
5. Epiphany, the consumate professional, yelling information in the hallway regarding Michael's surgery, when his anxious parents are standing in an open doorway & can hear everything she's screaming. First of all, a character like her would not do such a thing. Second, no nurse would get away with it without being reprimanded.
6. If a family is tightly knit like the Spencers/Corinthos/Qs, how come none were present during the operation? Why did Bobbie only show up after the procedure was done? Where was Lucas? Why wasn't Mike there?
7. Characters acting out of character (see #5 &6)
8. Port Charles community not reflecting true economic, racial, ethnic & religious diversity of American communities.