Clarification of Hold'em rules for split pairs

[Thirdman]

Hi,

I'm a bit confused on the rules of hold'em when there is a showdown with two players who both have the same split pair. Here is an example

player 1
A6

Player 2
A9

Board:

A X X X X

I've played a game where the outcome was a split pot rather than the A9 winning even though both players only had a split pair of aces. Can someone explain this please.