…No one had done anything with any Anchorpoints yet.

A: Anchorpoints are part of the timeline, so “latest” in this case means “latest in time” (farthest down the timeline). At the start of the game, the latest Anchorpoint will be D9. When that is flipped, it turns into an Anomaly, and the latest Anchorpoint is now D4.

As the game progresses, Anchorpoints continue to get flipped and turn into Anomalies, always the latest Anchorpoint in the timeline, such that the Anomaly “spreads” backwards in time from the end of the timeline towards the beginning.