Key forward McKernan played one of his best games against the Eagles, but is likely to miss several weeks after being reported for striking Sheppard with a raised elbow late in the first quarter.
"I'm disappointed with what happened because I thought he played a really good game," Sanderson said.
"He was marking the ball when other guys weren't and he would have been handy for us [next week].
"We're in the lap of the gods a little bit, but we'll just have to see what the result is on that one."
Saturday night's loss could see Adelaide slip three wins out of the eight, leaving a mountain to climb to reach the finals with only eight games remaining.
"We're going to find it really difficult from here, but we certainly won't be changing anything with the way that we approach any game," Sanderson said.
"Our next objective is to beat Collingwood at the MCG next Friday night.
"Externally there will be a lot written about where our season's at. Can we make it? Are we going to play finals this year? What we'll do internally is just focus on our next opponent."
Sanderson admitted his side lacked polish when it counted against a fast-finishing Eagles outfit.
Rory Sloane missed an opportunity in the goal square late in the game, while Matthew Jaensch and Tom Lynch also let chances go begging.
"It's draining tonight, 13 points up … I'm trying to come in here and be really positive, but I feel really disappointed for the team and the club," Sanderson said.
"You shouldn't let a game like that slip … fundamental errors at critical times which is disappointing.
"We just needed a point, any score would have done, we could have looked for ways to ice the game and we didn't do it.
"We missed too many shots in front of goal – nine goals, 15 (behinds) – we missed some absolute sodas tonight.
"In a close game you've got to go back and nail them."
While praising the club's defensive effort, Sanderson criticised the way Eagles players were allowed easy exits out the back of contests that ultimately led to the match-winning goals.
Harry Thring is a reporter for AFL Media. Follow him on Twitter: @AFL_Harry.