The Dutch defender’s header beat Fulham keeper Bernd Leno, who claimed Manuel Akanji had been in an offside position and that the City player had obstructed his view.
VAR reviewed the incident and awarded the goal – but City coach Lillo believes the rules are unclear.
“A similar thing happened at Sheffield United, and we thought the goal was offside in that game,” said Lillo.
“When they (match officials) gave their explanation, they said it was about being in line with the ball.
“I think our player, Manu in this case, was less in line with the ball than the goal scored by Sheffield United.
“That’s the explanation they gave us and that’s all I can tell you, but it needs to be cleared up.”
Asked whether he was enjoying management, Lillo smiled and said: “I want Pep here, although he was present with us today, always talking, before, during and after the game like last time.
“I’m glad we continued to win but not in the circumstances, we need him here and I miss him.
“He’s very reflective and reacts to what’s happening, even more so now he’s stepped away from things for a few weeks.
“We comment on what’s happening and debate as we do when he’s here in person. We look for a way together to find a way of moving on and enjoying the game.”
And on Jack Grealish’s injury, Lillo said: “It’s going to be difficult for Jack to make it for the national team call up. But I’m not a doctor and it would be difficult for me to explain.”