Moore, in his first assignment as coach of a Test nation after succeeding Australian compatriot Bennett King following the World Cup, was exasperated at the manner in which West Indies lost by an innings and 283 runs.
England went 1-0 up in the four-match series and may have inflicted some mental scarring as well. It was West Indies' heaviest ever Test loss.
The tourists were bowled out for 146 and 141 in reply to England's 570 for seven declared.
"It was ugly in the end and looked like a pretty meek surrender, though I thought there was some encouragement in the middle when (Dwayne) Bravo (52) and (Runako) Morton (25) were going well.
"Unfortunately Morton fell for the three-card trick and got out and after that it was a pretty quick exit. It was disappointing in the end.
"I think they get to a point where they don't actually realise we've got to play for five days. They need to bat the whole way through. We saw England do it and we've got to do it as well. I still have faith in all 15 of our guys," he added.
Moore said he was frustrated at the team's inconsistency after they battled for a draw in the first Test at Lord's.
"(This result) is a reflection of our inconsistency rather than a reflection of where the team is at.
"We get to a point where we hang in there like in the first Test and then unfortunately we get to a point when we can't string two innings together. We can be so good one Test and then very disappointing the next one."
A decision is likely to be taken on whether captain Ramnaresh Sarwan will stay on the tour on Tuesday after consultation with medical staff.
Sarwan injured a joint in his right shoulder after falling awkwardly trying to prevent a boundary on Friday.
Moore is hopeful, though, that experienced batsman Shivnarine Chanderpaul will be fit for the third Test, starting on June 7, after missing Headingley with tendonitis in his knee.
Places up for grabs, says Moore: West Indies coach David Moore said there "will certainly be questions asked on both the batting and bowling side" after what the Australian described as his team's 'ugly' second Test defeat against England here at Headingley.
West Indies have just a solitary tour match ahead against an MCC side in Durham which, while captained by Sanath Jayasuriya, is largely made up of student players.
So far the West Indies pace trio of Daren Powell, Jerome Taylor and Corey Collymore have carried little threat.
The tourists do have the likes of Fidel Edwards, Ravi Rampaul and Darren Sammy waiting in the wings of their 15-man squad and after Monday's mauling Moore said: "We've been looking since the first Test to see who are going to be the best bowlers to take us through.
"Over the last few games, the three we took into this game have been doing a job for us. In the Test series in Pakistan they did a reasonable job for us - and throughout the World Cup they did as well.
"But as always, at the end of every game you have to work out where your players are at and who's going to give us the best chance of winning a game.
"There will certainly be questions asked on both the batting and bowling side," he added.
Moore said there was no magic solution to West Indies' woes as the tour squad was the best available.
"They're the 15 best guys we could have picked - and they need to work hard to develop their cricket and confidence to get good results on the board."
And he insisted West Indies, ranked a lowly eighth in the world rankings and without an away Test win against major opposition since 2000, could yet fight back.
"We're still going to have a crack. What do you want us to do - lie down? We're not going to do that."