According to the Puppetmaster archtype the "A puppetmaster can cast spells from the bard and magus spell lists, and treats bard spells as magus spells."
The spell Heckle appears as a level 2 Bard Spell and a level 3 Magus Spell, and yet the very same page of Arcane Anthologies has a Magus Spell book with Bard Spells that lists Heckle as a 3rd level spell. Is this a mistake or does the puppetmaster have to cast Heckle as a 3rd level spell despite it being a 2nd level bard spell.
The Puppetmaster archetype doesn't specify how to handle situations where the same spell appears on both lists. I would agree that the puppeteer should be able to cast heckle as a 2nd level spell. The heckle spell appears twice on the puppeteer's class spell list, allowing him to take the more favorable level.
As for the spellbook, it's impossible to know whether this is an oversight or the author thought that the merged spell lists work differently than you or I are intuiting.