The Young Lions crashed out of the tournament in Italy after losing 4-2 to Romania on Friday.
Crystal Palace right-back Wan-Bissaka and Manchester City midfielder Phil Foden, who scored a wonderful solo goal in their previous game against France, were both dropped to the bench for the crucial game.
Wan-Bissaka’s omission came after he scored an injury-time goal in a 2-1 defeat to France three days earlier.
And talkSPORT host Cascarino has hit out at Boothroyd for failing to back the young defender, who is reportedly closing in on a £55million move to Old Trafford.
He told the Weekend Sports Breakfast: “I hated the decision on Wan-Bissaka, I thought it was terrible.
“You want trust from your team, you want your players to trust that the manager is going to back you.
“He [Wan-Bissaka] has made a mistake, one mistake in a game, if he’s your number one right-back, you play him again.
“All this talk of Manchester United and having his head turned, [it’s] nonsense.
“He made a mistake in a game, back him, tell him he’s still going to be number one. I think there were loads and loads of issues over the course of the two games.”
Wan-Bissaka made 35 Premier League appearances for Crystal Palace last season.
And he has been tipped for a senior England call-up in the future.
Cascarino added: “I watched him handle [Christian] Eriksen, [Eden] Hazard, [Alexis] Sanchez, he’s handled a good few wide men and he’s done it brilliantly.
“Now, if he’s going to be a scapegoat for the result against the French and on the day before the [Romania] game, we all knew he was out of the side, I found it really strange, I didn’t like it at all.”
Cascarino also criticised Boothroyd for leaving City starlet Foden out of his starting line-up, and has laid the blame for the Young Lions’ exit squarely at the manager’s feet.
“I clearly lay it down to the manager – it falls on him because of his decision-making in the games,” said the former Chelsea striker.
“You can’t change a team and have five players come in and leave out a player of Foden’s ability, who he is quite clearly England’s most creative player, when you’ve got to win a game.”