The league is playing with replacement referees after failing to reach a new deal on pay and pensions with the referees' association which was formally locked out in June.
The stand-in officials come from the lower divisions of college football, high school and semi-professional leagues and not surprisingly they have struggled with the complex rules and high-pace of action in the NFL.
While the week one refereeing was deemed just about acceptable by many observers, the second round of games involved plenty of confusion and brought criticism.
The worst of it came after the Monday night game between the Denver Broncos and Atlanta Falcons in which several calls were overturned, there were lengthy delays and a chaotic scuffle as officials looked on.
Even the ESPN television commentators, not normally ones to 'talk down' a game, expressed frustration at the lengthy delays, during a first quarter that lasted around an hour, and confusion which ruined a potentially entertaining contest.
"Honestly. It's embarrassing. The command and control of this game is gone," Mike Tirico said on air while his partner, ex-NFL coach Jon Gruden, said the game, which finished after midnight, was "hard to watch".
The worst spell came at the end of the first quarter when Denver's Knowshon Moreno fumbled and after a scramble, a Broncos player emerged with the ball only to find the officials had prematurely given an Atlanta recovery.
A scuffle ensued with the officials struggling to impose order and there was only a penalty given at the end of it.
The former vice-president of officiating for the NFL, Mike Pereira, who now works an analysis for Fox Sports, took to Twitter to vent his feelings.
"This is not the NFL I worked for. Don't care whose fault it is," he said.
Sunday's games had drawn plenty of similar criticism from those on the field and the sidelines.
Redskins head coach Mike Shanahan, whose side lost 31-28 to the St.Louis Rams, said he had been worried about the game descending into serious trouble.
"I've never been in a situation where you feel that there is going to be an explosion on the field. You're hoping that doesn't happen. It was very close to losing control," he told reporters.
After a chaotic and, at times, tetchy game against the Philadelphia Eagles on Sunday, Baltimore Ravens quarterback Joe Flacco told the New York Post that the replacement officials were "affecting the integrity of the game".
The criticism of Sunday's officiating from various quarters led the league to release a statement before Monday's game supporting the refs.
"Officiating is never perfect. The current officials have made great strides and are performing admirably under unprecedented scrutiny and great pressure," it said.
"As we do every season, we will work to improve officiating and are confident that the game officials will show continued improvement."
But Monday's messy officiating, in a high-profile game, will surely increase the pressure on NFL commissioner Roger Goodell to get back to talks with the regular refs.
According to a referees' association internal memo, published by the Baltimore Sun, the two sides have not met face-to-face for talks since September 1.
Another week of fans and pundits complaining about over-long and chaotic games and the pressure to end that stalemate will intensify further.