Millwall's Josh McQuoid suffered a knock in training and was left out of the Lions' season opener against Reading on Saturday, while Martin Paterson was substituted at half-time in Burnley's clash with Watford.
No official reason has been given for the withdrawal of James McClean, the Derry City forward who has been linked with Sunderland in recent weeks, with speculation that he could be set to switch his allegiance to the Republic of Ireland.
With first-choice striker Kyle Lafferty already missing from the squad with a hernia injury, the loss of McQuoid and Paterson is a headache for manager but McClean's absence is more worrying.
He won a first call-up from manager Nigel Worthington having caught the eye of a number of Barclays Premier League scouts with some eye-catching displays for Derry and, with no injury announced in a brief Irish Football Association statement, fans will be worried he is poised to join a growing number of Northern Irish players opting to turn out for the Republic.
Worthington said: "It is disappointing to lose players ahead of an important qualifier; but our focus remains on Wednesday night and the players available for the game against the Faroe Islands.''
The likes of Dan Devine, Darron Gibson, Shane Duffy, Marc Wilson, Daniel Kearns and Paul George are among those to have taken advantage of a FIFA ruling that allows players from the island of Ireland to choose which national side they represent providing they have not played for the other in a competitive senior international.
Although Worthington hopes to add Alex Bruce - twice capped by the Republic in friendlies - to the Northern Ireland ranks, the IFA have publicly bemoaned that the ruling has had a destabilising effect on them.
Three of the six forwards originally selected for the Faroes match remain available to Worthington, with Warren Feeney and the recalled Jamie Ward battling to join record scorer David Healy in the starting XI for what is a must-win match in qualification terms.