Jimmy Bullard drove a young West Ham side in front on eight minutes, but a header and a free-kick from Ian Hillier gave the visitors the victory.
The reserves, without Davor Suker who was on international duty, have four games left.
Coach Glenn Roeder was offering no excuses for the loss and says: "It was a young side we had out, but so did Tottenham - only Matthew Etherington and Dave McEwen - who played up front for the first team against us in January - were in for them.
"In the first 20 minutes having scored early it looked as if we would build on that lead and grab a victory, of which there haven't been too many this year.
"But we conceded a poor goal from a corner when one of our players lost a marker and they scored with a header which gave Billy McMahon no chance whatsoever.
"It was a disappointing goal to make it 1-1 at half time, followed by a piledriver which the goalkeeper had no chance of saving, but disappointing again to concede from a set play."
Scott Minto was a notable absentee and Glenn explains: "Scott had a slight thigh strain and with someone that has been out so long; other parts of the body are weaker through not playing football.
"Although his knees are fine, which has been the major problem, he has picked up this strain, but he should be back next week."
Glenn says he has some sympathy for the injury hit Christian Bassila, who, with Steve Potts and Shaun Byrne, comprised the only players with first team experience. Indeed, knee and family problems have meant we have only seen a fleeting glimpse of the combative midfielder and Glenn says:
"He's been like so many of our players this year, injured for large parts of the season. He got injured when he came on as a sub against Manchester United, needed an operation, and now he has been fit the last few weeks but the season is coming to an end.
"We haven't signed him full time, he is on loan, and obviously Harry will make a decision on his future at the end of the season."
One plus point was the performance of young defender Steve Laurie, and Glenn comments: "He has had three good games after a long time out injured, and Roger Cross has been impressed with him."
As for the first team's clash at Maine Road on Saturday, he says: "There is no reason to be fearful; everyone knows it will be a battle up there but you can get a lot of enjoyment playing those games.
"We have to resist the onslaught as a point is no good to them - all our thoughts lead to Maine Road, and it's an all or nothing game for Manchester City."
Team: B.Mcmahon, Clark (Etherington 82), Byrne, Laurie, Potts, Uddin, Ferrante, Bullard (Riddle 60), Bassila, Foyewa, Britton. Unused subs: J.Sealey, Smith.