I almost think Phillips was too smart of an actor not to have done so on purpose.
It may have gone something like this:
*EP reads the 'Caretaker' script*
EP: "I'm dating a two-year-old??
My character must be a pedophile."
Director: "Um, no, Ethan, she's fully grown."
EP: "A fully grown two-year-old? You sick freaks
Writer: "Ethan, I don't think you understand..."
EP: "Ohhh, I understand all too well!!"
Director: "Ethan, Neelix isn't a pedophile."
EP: "Have you read
this script? Yes, he is."
"FINE! Do what you want."
EP: (mumbles) "Stupid writers trying to pull a fast one on me."