Staff would in the past submit a handwritten teamsheet to match officials before kick-off, but they are now recorded electronically.
Holloway said the officials did not ask him to verify the team on a screen before kick-off, as he argued is usual protocol.
“When we used to write the teamsheet down it was never wrong, was it?” Holloway said.
“But when they get it on an iPad and it’s not shown to us, how can I say that is my team and I haven’t checked it?
“No-one’s checked it and it’s too late to check it when the game’s gone on and they noticed it because one of their staff noticed it.
“It’s a major whoopsie I would suggest from the officials – is that us, is that them?
“They’ve got to have a right good look at themselves. Why don’t we go back to the written ones?”
Luton took a seventh-minute lead through Jerry Yates’ penalty, before Will Wright equalised 30 minutes later and then Filozofe Mabete put Swindon 2-1 up in the 53rd minute.
Wilshere said he trusted that the EFL will “come to the right decision”.
“Whatever the rules are, the rules are,” he told BBC Three Counties Radio.
“I felt like the decision could have been made quicker – seven, eight minutes, it’s either we’re carrying on or we’re stopping – but the EFL will investigate it and they’ll come to the right decision.”
