Yes, that is the intention. For instance, if it says 3 sets of pushups, you do one set, rest, do the 2nd set, rest, do the 3rd set, rest and move on to the next exercise.
In Phase 2, she introduces Supersets, which are TWO exercises per set, for instance Bent-over Barbell Row and Seated Cable rows. So for Set 1, you do the set of Bent over Rows then immediately (no rest) follow by the Seated Cable Rows, the rest. Then repeat the two exercises again, then rest, and finish up with the 3rd set of both exercises before you move on to the next exercise.
In Weeks 11 and 12, you do all the sets of exercises in the list once for one circuit, then repeat all the exercises again for the 2nd and 3rd circuits.
Frankly, having done it both ways, I preferred doing circuits because by the time I got back to the same exercise, it felt like I could put more into it (rather than just having a minute rest in between the same exercise).