FORMER St Kilda player Stephen Milne will face trial on rape charges over an alleged incident in 2004.

Magistrate Peter Reardon on Friday ruled there was sufficient evidence for Milne to stand trial on three of the four rape charges.

The 33-year-old has been charged with raping a woman in the Melbourne home of former St Kilda teammate Leigh Montagna.

The Melbourne Magistrates Court heard that the woman, who was 19 at the time, thought she was with Montagna when the rape allegedly occurred in a darkened bedroom.

The committal hearing was told that Milne repeatedly tried to have sex with her despite her saying no to his advances.

Milne, who attended every day of the four-day hearing with his wife by his side, stood and showed no reaction when he was committed to stand trial.

He said only four words: "Not guilty, your honour."

The court heard the alleged victim and her friend met up with the two footballers after the club's family day event in March 2004.

The group headed to Montagna's Highett home, where all four later ended up in the same bedroom.

The complainant began kissing Milne on the bed, mistakenly believing it was Montagna.

Her friend said she decided to leave the bedroom when she heard the alleged victim say "no", "don't" and "stop it".

Montagna told the court he also heard the woman say no, but said he thought it was more in a "conversational tone".

The woman's friend, who can't be identified, then flung open the door as she left the bedroom, shining light on to the bed in a bid to defuse the situation.

The alleged victim said she then realised it was Milne with her in the bedroom and not Montagna, the court heard.

Both women said it was very dark in the bedroom before the door was flung open.

But Montagna said he had no trouble seeing everyone.

Police later checked the lighting in the room, with at least one detective agreeing the lighting was sufficient to make out someone's features.

Details of those lighting tests, however, never made it into the original police brief.

Charges were only laid in June after a police review found the initial investigation nine years ago was inadequate.

Milne's defence team spent days pointing out how police notebooks, text messages and some DNA evidence had gone missing and criticised the work of the initial investigation headed up by former detective Scott Gladman.

One of his colleagues testified that Mr Gladman got too close to the alleged victim and was even "quite flirty" with her, to the point where he reported the behaviour to their supervisor.

"There were times when I thought he had been talking with his girlfriend," Detective Senior Constable Steven Cornwill told the court on Friday.

"I thought he had an inappropriate relationship with her."

Earlier in the committal hearing, Mr Gladman had rejected that he had any bias and had ignored key evidence that tended to exonerate Milne.

"Absolute and total rubbish," Mr Gladman told court on Thursday.

The court heard that very little was added to the police brief in 2012 when the file was reviewed and police decided to proceed with charging Milne.

He now faces a trial, expected to be held in August next year, after a directions hearing on December 10.