Police have been accused of manipulating a photo of Jean Charles de Menezes so it could be compared to that of one of the 21/7 bomb plotters.
The image had been "stretched and sized" to form a composite image of the Brazilian and Hussain Osman to show the jury, prosecutors told the Old Bailey.
Mr de Menezes was shot dead after being wrongly identified as one of the men who targeted London's transport system.
The Metropolitan Police denies breaking health and safety laws.
Mr de Menezes, 27, was shot seven times in the head on a train at Stockwell Tube station on 22 July 2005, after being wrongly identified as Osman.
The Met Police said the composite picture was created to illustrate the difficulties officers would have had in differentiating between the two men.
But Clare Montgomery QC, prosecuting, told the court it had been altered "by either stretching or resizing so the face ceases to have its correct proportions".
Forensics consultant Michael George told the court that the police composite appeared to have a "greater definition" than the two images used to produce it.
He produced an alternative composite, which was shown to the jury, in which the two faces had different skin tones and their mouths and noses were not aligned.
Ronald Thwaites QC, defending, asked Mr George whether there had been any manipulation "of the primary features of the face".
Mr George replied: "I don't believe there has been any... but making the image brighter has changed the image."
The court heard the composite was compiled using a 2001 identity card photograph of Mr de Menezes and a photo of Osman taken by police in Rome, where he was arrested.
The judge, Mr Justice Henriques, told the jury that a "serious allegation has been made that a picture has been manipulated so as to mislead".
Earlier, Mr Thwaites cross-examined immigration official Paul Roach over a counterfeit stamp found in the Brazilian's passport, asking if this meant he had been in the country illegally.
Mr Roach told the court Mr de Menezes first entered the country on 13 March 2002 and was given six months' leave to remain, before extending his stay, as a student, to 30 June 2003.
The next record was of him arriving in Ireland from France on 23 April 2005 but there was no notification of when he returned to the UK.
The court heard how as a person entering Britain from Ireland, he would have had an automatic three-month leave to remain which at the earliest would have run out on 23 July, the day after he was killed.
A counterfeit stamp found on his passport may only have been added after he entered the UK, Mr Roach said.
The trial continues.