Borthwick-Jackson has just signed for Oldham Athletic, while Wilson is with Joyce's Salford City.
Joyce told the Manchester Evening News: "When I was there you were mindful of where people went and what the managers and coaches at the football club were like.
"You always tried to put them in the right place to help them through. I think for a spell after Sir Alex left we lost a bit of control with the loans and some were more to do with recouping the wages and a loan fee.
"I look at particularly James Wilson and Cameron Borthwick-Jackson, both were mismanaged with what happened to them loan wise and they should have had better careers at United.
"It wasn't their own fault, you can get the wrong place at the right time for the wrong reasons and it doesn't help their development, when people needed certain things to help them progress further."