The former Celtic attacker was given a run by manager Roberto Martinez in the shock loss.
"The result was obviously not what we were looking for," Maloney told the Wigan Evening Post. "We made a few changes but, to be fair, so did Palace so I certainly wouldn't be looking to use that as an excuse.
"Our first-half performance cost us because, although we started well, they stepped up and we couldn't respond.
"There was a big improvement in the second half, but it wasn't enough."