Immediately after the match, Wilkinson admitted he was mystified as to what went wrong given he felt he had been kicking the ball sweetly.
Argentina also had their problems, with Felipe Contepomi and Martin Rodriguez missing a total of six penalty kicks under the permanent roof at the Otago Stadium.
England have been playing with the Gilbert Virtuo ball, albeit with a red rose linery, since the 2010 autumn internationals and through their home Six Nations matches.
The ball has also been used in the Tri-Nations. All World Cup teams were provided with 15 to use in preparation for the tournament and a further 30 on arrival in New Zealand.
But Johnson suggested the World Cup batch is different, indicating the match balls behave differently to practice balls because they have not been kicked-in.
"Jonny thought he hit it pretty well. The detail of the ball, it's not my area but they are slightly different. We have seen some kickable kicks missed over the weekend,'' said Johnson.
"We have got some ideas on it. Maybe the balls feel slightly different when they are new, potentially, than when they have been kicked quite a bit.
"We haven't got any hard evidence, it is maybe a gut feeling. I don't know the detail of the quality of the build but to me they feel slightly different. Whether that is true or not, I don't know.''
Andrew Challis, Gilbert's international brand manager, confirmed the balls had not been tested in an indoor stadium, such as that in Dunedin.
But he defended the performance of the Gilbert ball and insisted the company retained full confidence in it.
"It is not possible for the balls to be different,'' said Challis. "All balls are made from the same production line, the same materials, the same processes. The only difference is a cosmetic one (the World Cup design).
"If that is Martin's feeling I can't contradict him.
"We produce a ball that is constant. It is hand-checked by us before it leaves. They are numbered and used in the captain's run by both teams.
"Our confidence in the ball is absolute."
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