Last night's Carling Nations tie with Northern Ireland was overshadowed by the furore surrounding the 20-year-old's absence, with the FAI and Wigan now seemingly embroiled in a dispute which could have grave implications for McCarthy's Irish situation.
On Monday, Trapattoni said he had heard nothing from the player, while FAI officials briefed that "seven or eight" attempts to make contact with the player were unsuccessful.
Statements from Wigan manager Roberto Martinez and the FAI yesterday have only succeeded in muddying the waters.
Once again, the lines of communication are blurred between the 72-year-old and the highly sought-after £20m-rated talent, whose actions have left the Italian far from impressed.
They had clear-the-air talks in March to iron out confusion that existed about his international allegiance.
However, two months later, McCarthy was among a number of targets in an impassioned outburst by the "bitter" Trapattoni about the attitude which some young players have towards international football.
A further round of discussions may be required to move past what has developed into an unfortunate incident -- with plenty of questions still lingering.
1 How did this come about?
On Monday afternoon, in his pre-match press conference ahead of last night's game with Northern Ireland, Trapattoni vented his anger at some absentees and referred to one player who hadn't answered his call-up yet. It was later confirmed to be McCarthy, with FAI sources briefing that "seven or eight" attempts to contact the Wigan lad had been met with no response.
2 What is MCCarthy's excuse?
A family source says that McCarthy suffered a knock in Sunday's win over Stoke that clinched Premier League survival, went out with his team-mates to celebrate staying up, then went for a scan in St Helens hospital on Monday morning. Martinez yesterday said that the results of the test revealed grade one ligament damage -- a setback that means three to four weeks on the sidelines.
3 When were the FAI informed?
It has now emerged that the FAI's medical staff were informed via a text from Wigan on Sunday night that McCarthy required a scan. An FAI statement has confirmed that they have received the results of the scan.
4 So, what's the problem?
The missive from the FAI added that, in the opinion of their medical team, led by Dr Alan Byrne, the scan didn't show any serious damage at all. So, they responded to Wigan asking when McCarthy would be reporting for duty. As of last night, they said there had been no further official correspondence -- effectively stating that they didn't believe the players 'injury' justified his absence.
5 What now?
Trapattoni is clearly unimpressed. He made it clear on Monday that unless a player is seriously injured in hospital or "dead" then he would expect them to report for international duty and let the FAI doctors have a look. Sean St Ledger and Darren O'Dea were commended for reporting to Dublin with injuries, although neither were involved in club activity last weekend.
6 Did McCarthy have a flight booked?
FAI officials on Monday were suggesting that attempts to get in contact with McCarthy over the past number of weeks were unsuccessful. It is standard procedure for the international department to get in touch with players the week before a gathering to figure out their flight details and other travel logistics.
Unconfirmed reports say that McCarthy was booked on a 10.0 flight on Sunday evening -- a strange one, considering that other players involved in the Premier League climax weren't scheduled to come in until Monday or even later.
7 Why has McCarthy not spoken to Trapattoni directly?
This is a difficult one for the player to answer. McCarthy is in an environment where players have everything done for them, and he was fighting a relegation battle with Wigan, but after confirming his international loyalty to Ireland in March and receiving a hero's welcome at the Aviva Stadium, Trapattoni expected a greater show of desire. If it is the case that McCarthy went off the radar and presumed that someone else would sort it out, then it's a naïve decision that could prove costly.
8 Will this have an impact on his future involvement?
Rewind 12 months and McCarthy missed another end-of-season gathering. He came to Dublin, met with Trapattoni, and said he was fatigued after a long debut campaign in the Premier League with Wigan.
However, that didn't seem to satisfy Trapattoni, who excluded him from the senior squad last autumn. It's understood that McCarthy was aggrieved by his absence without explanation. Another period of exile seems likely with Trapattoni saying last night "he had to decide" whether to call the player in again.
9 Would McCarthy have been involved in Macedonia on Saturday week?
In all probability, no. Given that it's an away qualifier, Trapattoni will go for a more experienced option in the centre of midfield and is unlikely to experiment with his formation.
Indeed, it's more likely that McCarthy will have to wait until the World Cup 2014 qualifiers to establish a place in the team. But there's no doubt that Trapattoni would like to have him as an option from the bench.
The FAI's statement suggests they believe that his injury isn't a serious enough reason to keep him away.
10 What will the other players make of this?
Members of the squad are sick and tired of the headlines being dominated by players who are absent, a consistent feature of the past couple of years. With Stephen Ireland it was a serious issue, which made it harder for the player to come back and face the grief.
McCarthy is a completely different kind of character, a quieter type who doesn't have too many friends in the Irish set-up yet. He would know Seamus Coleman and one or two others from the U-21s but he still isn't fully bedded in to the dressing-room banter. Senior players will look on this sceptically.
11 Where do we go from here?
After failing to get off on the right foot, it was assumed that any tension that existed between Trapattoni and McCarthy were resolved in a face-to-face meeting in March. McCarthy was relieved that all the speculation about his international loyalty was finally, in his words, "put to bed". Now it's become a burning issue again.
The haphazard handling of the past 48 hours -- the claims and counterclaims -- mean that the next time he is named in an Irish squad, his presence is essential to silence those who doubt his commitment to the cause; a group which, not for the first time, appears to include Trapattoni.