Bayern Munich were indignant in the wake of a hamstring injury Arjen Robben aggravated at last summer's World Cup in South Africa that kept the Dutchman out for half of last season.
Furious Bayern chairman Karl-Heinz Rummenigge claimed it was time all national sides insured players against injury and called into question the right of FIFA to insert set periods in the season when clubs have to release players.
United returned from their five-match tour of North America knowing that immediately after next Sunday's Community Shield encounter with Manchester City at Wembley, they will lose players to international friendly matches.
Three weeks after that comes the first international double-header of the new campaign, within a month of that there will be another and in mid-November their players will be called away once more.
Yet Blatter has spoken about more international dates being added, which has angered Europe's powerful leading clubs intensely.
Although he accepts resolution will not be easy, Gill does not see the present situation as sustainable given it is the clubs who own contracts and invest millions in their squad.
"There are some issues," said Gill.
"The way the calendar is constructed, the number of dates FIFA put in, insurance.
"There are no easy solutions. These things have been around for many years but if we can get together, it will be for the betterment of the game."
It could be argued FIFA have more than enough on their plate just now trying to solve the corruption scandal that erupted in the wake of a presidential election in which Sepp Blatter ended up as the only candidate, although Gill trusts UEFA president Michel Platini to take up the cudgels on his member clubs' behalf.
"Clearly it hasn't been a good year for FIFA," said Gill. "No-one could say it has.
"Hopefully through some of the things that are happening, we can get the change and improve the organisation going forward.
"UEFA is a professional organisation. What it has done in terms of its own structure and the Champions League is very professional.
"We have had an initial dialogue with them and they can liaise with FIFA.
"The calendar is wider than just the European situation but it is clear: we provide the players. We are a key part of the game.
"The Champions League is one of the top competitions in world football. We are producing the product. Everyone has to understand that."
The row will doubtless rumble on for a while yet, with Gill now on standby for the next month just in case a deal presents itself that would solve Sir Alex Ferguson's midfield conundrum in the wake of Paul Scholes' retirement.
Even without Scholes, United have still been installed as favourites to continue their domination of the Premier League by registering Ferguson's 13 title and the club's 20th overall.
"The whole Premier League has been the greatest era for Manchester United," reflected Gill.
"Sir Alex has had some great teams within that. He did the Treble in 1999 and won the league the next two years.
"It has been fantastic. No-one would doubt that.
"But you could say in 1999, Arsenal and ourselves were ahead of the other teams. Then Chelsea came along. Now we have got Manchester City. Liverpool are coming back...Tottenham.
"We have been very successful but the most important thing is that the whole club, on and off the field, cannot assume it will continue.
"We have to continue to work hard and ensure the next five years are equally successful."