Hints: Something is Off

Getting started:
Some of these puzzles have a completely symmetric layout, but their solutions are clearly not symmetric. For example, the Skyscrapers puzzle is rotationally symmetric, but clearly rotating any solution gives a different grid.
Stuck after solving the logic puzzles:
Each word pair was meant to be part of a common phrase, but something is off about each word. You might want to look at the QUACK and DITTY pair for an idea.
Stuck on the final cluephrase:
There is a mathematical operation that works on 3D solids satisfying your clue phrase. This operation is its own inverse.