Town went in at the break 2-0 down, before conceding midway through the second half.
Jones said: “Since Fulham, all we have talked about is their crossing ability, stopping the cross. Defending with an extra number in the box and you need to show resilience and resistance to see out those moments, to stay in the game and to have a chance and we had a mountain to climb from minute one.
“I could see early on we weren’t going to cope – I had plan B and plan C in my head, like I have all season, but ultimately you need to show resilience and resistance. That was disappointing and we got off to a really difficult start.
“You have to feel like you’ll win a game of football and I think the senior boys, the men, with the greatest respect to the ones who are more mature, we all looked fatigued.
“I got the physical stats from Fulham, they were through the roof and we didn’t recover. I think the senior boys dig in and manage to give you a level, competitiveness. I am not saying we had the spark in the final third because we didn’t. But getting off to that sort of start, not making it difficult for the opposition, that was an area where we went wrong today.”