Elon Musk's X was billed by the city of San Francisco after the social media company's unauthorised flashing sign was taken down on Monday.
The X sign was placed on the roof of the company's headquarters on Friday, but 24 complaints were sent to the San Francisco’s Department of Building Inspections over it, media outlets reported.
Among the filings were complaints that the sign was a nuisance and its flashing lights disturbed nearby residents' sleep.
The company formerly known as Twitter will also have to cover the cost for the department's investigation.
City officials last week had also issued a notice to X Corp for installing the sign without first receiving authorisation.
The giant X appeared on the roof after workers were temporarily halted by police last week from removing the company's previous bird symbol from the side of the building.
Replacing the logo would require a permit to ensure safety conditions and that the building's historic nature was preserved, said Patrick Hannan, a spokesman for the Department of Building Inspection.
Twitter rebranded itself as X last week in a move that could wipe out billions of dollars in value for the company.
Mr Musk has a long-standing fascination with the letter X. The rebranding is part of Mr Musk and chief executive Linda Yaccarino's plans to develop X into an “everything app”.
In a tweet last year, Mr Musk said buying Twitter was a way to accelerate creating the everything-app X.
Mr Musk said X had received offers to move its headquarters of San Francisco, but stated that the company would not move.