Your score on those is not important. Try not to make anything out of scores until you are taking practice exams at near readiness. Phase I covers predominantly information from just that section, but Phase II and Phase III were designed to incorporate information you may have not yet reviewed. It's for early exposure as well as incorporating some stress into homework, because after all, homework is meant to prepare you for the exam, and the exam will have a few stressful flareups.
The goal of Phase II is to emphasize time-aware testing while mixing different topics into the passages. You are going to eventually review that material, so introducing a few questions prematurely will help later on with your review. And the MCAT mixes subjects, so it's good to get used to that. Out of the three phases, about half of the passages will be from that section exclusively and the other will mix things (from other chapters and occasionally other subjects). Treat it as a learning experience rather than anything diagnostic.
Our goal is to help you deal with weirdness more than it is to give you a score that means anything. Always keep in mind that what really matters is what you would get if you got that passage, or one just like it, on your MCAT. This approach has worked quite well for people, so deal with it as best you can knowing it's helping. As you review more and more, it will feel less unexpected.