Arsenal boss Jonas Eidevall dubbed the scenes "very weird" after the goalposts were adjusted ahead of kick-off after being deemed 10 centimetres below the appropriate limit.
And there was more controversy when Eidevall was misinformed on concussion protocols, leaving Arsenal to defend their 1-0 lead with 10 players on the field after Beth Mead's enforced removal.
"It's been a very weird experience being here," Eidevall said.
"Playing against a big club like Ajax where we had to measure the goals before the start of the game... I have never experienced anything like it to be honest.
"It's very weird but we can only control the things we can control."
When Mead's head clash forced her off the field, Arsenal were denied a concussion substitution, despite Eidevall originally being told he would have one.
"There is no doubt that Beth Mead needs to be taken off," Eidevall said.
"The problem I have is that I asked the fourth official if we could do a concussion substitute and she says 'yes'.
"We were preparing Lina Hurtig [to come on] then when we are going to do it she says 'no'. We were getting her ready for two or three minutes.
"We would have spent that time speaking to the players about how we could defend with 10 players. That misinformation from the referee -- I honestly don't know why and how that could be. It's such a simple question to answer yes or no."
Arsenal won the match 1-0 to advance to the Women's Champions League group stage with a 3-2 aggregate victory and will play their group stage matches at the Emirates Stadium.