Vexen rarely had to deal with puzzles. Zexion's vanishing acts were a small one – he'd go off to who knows where, and return with a bit more information… and something off about him. A half-gone smile or a faint dusting of a blush along his face. Nothing he cared about, but would he ever stop disappearing? The Replica project can't advance without someone to piece it together…
Only when the Riku Replica (who was his work alone, mind you) asked if it was alright to kill Zexion (apparently for being around Naminé, of all people) did the puzzle begin to fall together.
For the time being… "No, you can't kill him. He still has to clean the laboratory."