Hundreds of members of the Royal Navy, Royal Marines, Army, and Royal Air Force took part in the Armed Forces Day event staged at half time on Saturday.
Police are understood to have been sent footage and photographs of the event that have created a storm on social media sites.
Some complaints focused on fans' singing of Derry's Walls and a chant about the death of the IRA hunger striker Bobby Sands.
Military personnel were filmed dancing and applauding in front of singing fans before Rangers went on to beat Stenhousemuir 8-0.
Senior personnel from each branch of the Armed Forces watched on from the Directors Box.
George Galloway, the Respect MP for Bradford West, was among the critics, causing a storm online as he said he would raise what he described as "Scotland's dirty deadly secret" when Parliament reconvened and challenged First Minister Alex Salmond to comment on what he described as "the hate-fest of sectarian bigotry" and the Defence Secretary Philip Hammond to comment "on the participation of uniformed soldiers".
He later said he had received death threats, that there was a threat his wife would be raped, and that his family were demanding he cancel his forthcoming planned tour of Scotland.
"If ONE Muslim on Internet made ONE death threat against ANY British MP they would already be behind bars. Hundreds against me in Scotland?" he tweeted
The MoD said any personnel involved in misconduct would face disciplinary measures and possible police action.
"The Army and Police Scotland, assisted by Rangers football club, are investigating these complaints. Sectarianism is a breach of the Army's strict values and standards," said an MoD spokesman.
A spokeswoman for Police Scotland said: "We are aware of concerns raised regarding the conduct of a number of people attending the Rangers versus Stenhousemuir game at Ibrox on Saturday and these concerns are being investigated."
An MoD spokesman said: "We are aware that Police Scotland are investigating an allegation relating to the behaviour of some fans at Saturday's game at Ibrox.
"It would be inappropriate to comment further at this time.Any personnel found to have fallen short of the armed forces' values and standards will be dealt with by the chain of command and, if necessary, by the police."
But the claims were questioned by the Rangers Supporters Trust, which said one particular video posted did not contain any illegal and sectarian chanting.
The Trust tweeted: "Rangers fans should stop singing Derry's Walls the same day Scotland fans stop singing Flower of Scotland.
"Is singing expletives about 'Proud Edward's Army' at a Scotland match ok?"
Derry's Walls is a song from Northern Ireland about the 1689 Siege of Derry, which was part of the Williamite War waged between the Protestant William of Orange and the Catholic King James II.
Rangers could not comment further on the allegations given the police investigation but pointed out that the day was designed to "honour" members of the Armed Forces.
In a statement, the club said it had been proud to welcome more than 400 personnel from the Armed Forces to Ibrox.
It added: "The club has always been fully committed to honouring those who sacrifice so much for their country."and