Steve Clarke's side have been in superb form at the Hawthorns so far this campaign, winning seven of the 11 games in front of their own fans, helping them to seventh in the Premier League.
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"I don’t understand why they did that. You can tell that Brunt, the same as a lot of us, misplaced some passes, but the effort was still there," Jones told reporters.
"He was challenging and working hard. It was one of those days for us individually and as a team, we know that and we’ll learn from that."But Brunt’s a great player, he has been in the past and still is now. He’s a massive part of the starting 11 and the squad."
The side were also booed off at half-time and full-time during the defeat and Jones feels that they are in danger of becoming victims of their own success.
He added: "The expectations we’ve put on ourselves, and the performances we’ve given in front of the home crowd, means they expect that.
"We expect high standards from ourselves, but against Fulham it wasn’t a good performance.
"Yes, there were misplaced passes and mistimed tackles, but all the lads gave it a right good go."