There are no "missing" puzzles that hide or disappear. Professor Layton and the Last Specter (US) / Spectre's Call (EU) has a fixed set of 170+ puzzles always in the same locations. If you haven't solved one, it's still exactly where it always was.
Tip: If you're missing the weekly puzzles, they were distributed via Nintendo WFC (shut down 2014). They are unobtainable legitimately now. A complete save file from the internet or homebrew (NTRBoot/CFW) is the only way to access them today.