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."
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.