Lampard finally reached his double century for the Blues after a month stuck on 199 with a first half header against his former club at Stamford Bridge on Sunday.
But the 34-year-old's goal was greeted with anger by West Ham's travelling supporters as Lampard and John Terry celebrated the milestone in front of the away end.
Terry, who started the match on the substitutes' bench, already responded to taunts from the east London club's fans as he warmed up in front of them by bending over to aim his backside towards them.
And the atmosphere turned even uglier when Terry and Lampard, who were hated by West Ham supporters since leaving for Chelsea in 2001, were greeted with projectiles thrown onto the pitch following the 19th minute goal.
It was claimed Terry was hit by a coin and fourth official Howard Webb told Benitez to instruct Chelsea's substitutes to warm up away from the West Hams fans after that.
'Better in another part'
But Blues interim manager Benitez was adamant the unsavoury incident should not detract from Lampard's achievement, which moved him within two goals of Bobby Tambling's club record.
"When you score 200 goals you don't think too much about where you are celebrating, but after that you think it would have been better to be in another part [of the stadium]," Benitez said.
"We said it would be better if they do the warm-up on the other side. Howard Webb told us. I don't know if it was his decision."
Benitez's relationship with Lampard hardly got off to the best start when he went public with the news that the midfielder would be allowed to leave at the end of the season.
But he grew to admire Lampard's professionalism, installing him as captain against the Hammers and admitted only Liverpool's Steven Gerrard could match his influence over the last decade.
"I'm just happy he has scored 200 goals. It's a fantastic achievement for any player, especially someone like him," Benitez said.
"Since I came to this country people have asked me about Gerrard and Lampard. Both are great players … We are talking about Lampard and you can see him training, always working hard. There are plenty more games left so hopefully he can score more."
'Not a bad week'
Benitez, whose tenure with rivals Liverpool caused much angst among the Blues faithful, was at last able to create a more positive mood around the club this week.
Last weekend's comeback to force an FA Cup quarterfinal replay against Manchester United was followed by overturning a first-leg deficit to beat Steaua Bucharest in the Europa League last 16.
The win over the Hammers also moved the Blues above Tottenham into third place in the Premier League.
"It's not been a bad week," Benitez said. "If the team is playing well the fans will enjoy it. That is the main target for us.
"We have to stick together and make the right results. I'm really pleased with the atmosphere and really pleased with the team."
Meanwhile, West Ham are only six points above the relegation zone after their fifth defeat in their last seven matches.
But boss Sam Allardyce refused to be downcast, insisting instead that few teams could have lived with Juan Mata and Eden Hazard, who laid on Lampard's goal and then netted the second with a fine finish early in the second half.
"Chelsea were the better team," Allardyce said. "It was a tough afternoon against talented players, Mata and Hazard were both outstanding. You can't defend against that." – AFP