I don't see these scenes as plot holes necessarily, but just food for thought. Maybe Michele was getting even with Rafael for revealing her as a Cause member to Fernando. Or she thought it was a better strategy for both of them, since she had already been suspected to be part of the Cause and would be interrogated the most. You could also explain why she waited to kill Ezequiel simply: because she thought she would get away with it. Or maybe it meant to show that she doesn't really believe in the Cause, since the pill was meant to be kept for herself.

I think Fernando is smart but doesn't believe in the Process. He was forced into it by his father, and cares more about other people than succeeding. It doesn't make sense to pass someone who would bring the wrong attitude to the Offshore - they want people who blindly believe in the Process, as it's necessary for its survival. I believe that scene shows flaws in the Process, not the writing.

A plot hole I noticed was with Marco's family - how did the parents have so many kids before the age of 20? Another was at the end, when Joana storms out of final test and shoulder bumps Cassia. Later we see Cassia optimistically asking Ezequiel about the test: "So how did it go?", when it should have been obvious. Overall I think the show makes up for its mistakes with an intricate plot, great music, and interesting characters.