The Protectors had looked firmly in control of the game, holding a 3-1 lead with just five minutes remaining.
However, Tatsuro Inui pulled one back with a delightful freekick after Kenji Arai had felled Mislav Karoglan on the edge of the area, before Fazrul Nawaz raced through to grab an unlikely equaliser minutes from the end.
Having previously identified his side's defence as their main area of weakness, Lee was once again left frustrated at the final whistle.
"I'm disappointed," Lee said after the game. "I already [knew] we have a problem in defence, that's why I tried to fix it during practice, but we made mistakes."
Lee also believed the Warriors should not have been awarded the freekick that led to their second goal, while he suspects Fazrul's equaliser was scored in an offside position.
"I don't want to make excuses but I'm just wondering why they got the freekick as Kenji had already touched the ball," Lee bemoaned.
"The third goal we conceded looked like it was offside. I cannot say for sure, that's why I need to check."
There was some positives for Lee to take however as his charges looked fluent in attack, with Qiu Li and Shotaro Ihata combining for Home's three goals, although it was another fruitless night for Frederic Mendy, who came off just before the hour mark.
"As you saw, our three goals were wonderful," Lee added.
"[In the] last two games, Mendy and Ihata haven't scored. Unfortunately, Mendy still hasn't been able to score, but Ihata scored tonight [Sunday].
"But the problem is our defence."
Sunday's match also saw the return of Indra Sahdan Daud to the Home starting XI, and while the former Singapore international failed to score, he laid on a classy assist for Ihata and Lee expects more from him in the coming weeks.
"Even though he [Indra] didn't score, I believe he can play better," Lee said.
"That's why I will give him chances to play."
Lee will be hoping his charges can bounce back in time for Wednesday's opening AFC Cup Group G game against Hong Kong's Citizen.