Take a module like The Dance in the Blood. In Manesty (pag. 16) I see 7 possibile clues plus a core one. The first seven clues require a 1-point spend or not? Are some of them zero-spend? Do I just decide based on what the players say and how they role-play?
So, one thing that both clarifies and obscures how spends for clues work are scenarios. Part of this comes from different play and design styles for individual writers. This is fair enough--there are a number of ways to approach dispensing clues, depending on personal Keeper and group taste, etc. (A similar variance happens with any game system, but it's a bit more obvious in GUMSHOE.)
Your example here is from a Graham Walmsley scenario. His particular view is that core clues are free but any other clue requires a 1-point spend. So in Manesty,seven of the clues cost one point each, and the core clue is, of course, free.
In THE DYING OF ST MARGARET'S and THE WATCHERS IN THE SKY, the first two scenarios of his, this is explained in the introductory material. I only have THE DANCE IN THE BLOOD as part of THE FINAL REVELATION collection, so I don't know if that had the same sort of explanation when it was published by itself.
Basically, it's just Walmsley's scenarios that are presented in this style. In other scenarios, point spends are called out and specified. You may see a reference to Library Use finding the book, a 1-point Latin spend translating the information, and a 2-point History spend noting that a particular passage contradicts established history wildly. So, you as Keeper know you are dealing with clues that 0, 1, and 2 points respectively.
It was in published scenarios that I first realized that a non-core clue didn't necessarily require a point spend. The inference I (and many others) make when reading the rules is that core clues are free and that other clues require spends. But the actual situation is that while all core clues are free, not all free clues are core clues.
As for how you should handle Manesty and the rest of that scenario, make the core clues free. As for the others, you can either charge a point for each of them (which is how it was designed) or vary it as you like. Certainly, it's easiest, especially while getting used to the system, to just charge a point each time.