Is it just me or does the CFAI morning version B mock exam leave out certain sections?

Yeah, the breakdown on the mock they have on there is wierd.. My morning session had no fixed income, equities, derivatives or alternative investments. Breakdown was 48 FRA questions, 24 econ, 19 corp finance, 18 ethics, 11 quant.. and then the PM section had no FRA at all.. Strange way from them to break up the questions.

Yes, that is the case because CFAI (in their great wisdom) sort of treated the two item-set mock exams as one single day-long session (even though the actual Level III has the essay type questions in the morning) — so they weighted the topics between them accordingly.