The MTA and United say they didn't know that the ad would offend some victims and survivors of 9/11.
A United Airlines ad across the street from ground zero that read "You're going to like where we land" has been removed after NBC New York reported that some found it inappropriate.
Some New Yorkers said it was insensitive because of its proximity to where United Flight 175 struck the south tower on 9/11.
The MTA approved the ad and said it was a third-party vendor that put up the sign above ground at the Cortlandt Street R subway stop, directly across the street from the terror attack site.
See exclusive photos of the ad here, and get a look at what replaced it.
The ad was part of a wider campaign for United, which apologized on Wednesday for another 9/11-related controversy -- putting back into circulation the flight numbers from the Sept. 11 planes.
Flight 175 took off from Logan Airport in Boston, carrying 51 passengers, nine crew members and five hijackers. It hit the south tower at 9:03 a.m.
The MTA told NBC New York on Thursday that it was contacting the vendor "to remove the ad from that location as soon as possible" and it was already gone on Friday.
A United Airlines spokesman said the airline was not aware of the ad's placement, and said it was part of a campaign that was launched in March.
The airline lost 18 workers on 9/11.
Mike Burke, whose firefighter brother, William, died in the tragedy, said the ad was a poor choice.
"It's pretty tacky, pretty unfortunate," he said.
Pedestrians in the area said the ad's message didn't seem to be deliberately controversial, but could be seen as insensitive to victims and survivors of the 9/11 attack.
"It brings back very bad memories of 9/11 and I don't think this is an appropriate place for that kind of sign. I think they should be more considerate of the people who died here," said Annette Guadalupe of Ozone Park, Queens.
"I think it's just ignorance, it's not malicious, just ignorance," said Ross Ouellette, who lives in downtown Manhattan.
Some passersby said they hadn't noticed the ad -- or the potential controversy it could stir.
"I walk by here all the time and I've never noticed it," said Eric Poon.
The debate comes a day after United -- which is in the midst of a merger with Continental Airlines -- apologized for reusing the flight numbers of two hijacked planes used in the 9/11 attacks.
Flight numbers 93 and 175 were mistakenly assigned to two flights by Continental Airlines.
"We are taking immediate steps to remove them and apologize for the error," a United spokesman said.