The young left-back was recently recalled from an impressive loan stint at Colchester United where he racked up 20 appearances and contributed three goals during the first part of the season.
"He has got a big opportunity now," Stubbs told evertonfc.com.
"It is in unfortunate circumstances but when you look at it from the other side, that's football. When one door closes, another one opens.
"We are obviously disappointed for Bryan and the way it's come about but it is an opportunity for Luke now.
"He has done really well at Colchester and the manager has been very impressed with the way he has played and improved his game."
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