Striker Alvaro Negredo had been readied to come on in the second half of Sunday's 3-1 loss at home to Atletico Madrid in La Liga, until he was told to return to the bench.
Suggestions surfaced that he bowed to fan pressure at Mestalla, before eventually introducing the player, yet Neville refuted such claims and blamed Aderlan Santos' red card for the confusion.
"I have nothing to add about the substitution on Sunday," he told reporters as Valencia prepare for Thursday's Europa League last-16 tie at Athletic Bilbao.
"I had not seen they had sent off [Aderlan] Santos, I was talking with Alvaro to send him on and I changed my mind when the sending off happened.
"There was a moment of confusion. We were thinking for some minutes. I have the right to do that.
"When we lose it always seems there is something to pick on, we had played well for 70 minutes. This is something absurd which had no effect at all on the result."