He was charged with possession of marijuana in 2000 when police were investigating a burglary at his residence, but the charges were dropped due to a lack of evidence.
Harbaugh was asked Monday if McAlister is in the dog house.
"We don't have a dog house around here," Harbaugh said. "If you see a doghouse, let me know."
When asked Sunday why he was only involved in a handful of plays, McAlister replied: "Go ask the coach. I don't have an answer for you. He'll tell you. If I don't start next week, it's up to him."
Harbaugh alluded several times Sunday to McAlister's recurring knee problem while stressing that there hadn't been a new injury.
However, McAlister wasn't listed on the injury report prior to the Dolphins game.
When asked Monday how his knee was feeling, McAlister replied: "My knee is excellent."
McAlister told friends Monday that he's not worried about the situation.
McAlister was eating lunch in the cafeteria Friday while the rest of the team was practicing outside.
Harbaugh said that McAlister did participate in Friday's practice, though.
"I can't remember exactly what the numbers were, but he practiced Friday," Harbaugh said.
On Sunday, Harbaugh emphasized that McAlister wasn't being disciplined.
"Chris has played well, he’s really worked hard this year," Harbaugh said. "There hasn’t been a situation where there has been an injury, but there has been some wear and tear on it. It’s not a matter of starting or not starting, it’s what packages we put him in to be most effective.
"You’ve got to practice all week to play on Sunday, but we can’t overload that knee. He could be out there starting next week. We’re always looking to put the best players on the field. We had a tough game last week, we didn’t play as well as we wanted to, but Chris had a great week at practice last week."
With McAlister's status up in the air and cornerback Samari Rolle hopeful of returning to the field as soon as this week as he recovers from neck surgery, Harbaugh praised Washington and Walker for their work against the Dolphins. Quarterback Chad Pennington passed for 295 yards with one touchdown pass, and linebacker Terrell Suggs returned an interception 44 yards for a touchdown.
McAlister could reemerge as a starter at some point, according to Harbaugh.
"I think Ted Ginn runs about 4.3, right? So, Fabian only had to slow down just a bit to cover him and he did a great job," Harbaugh said. "And Frank played a good solid game back there. So, the opportunity to develop some corners is a plus.
"But Chris is still very much in the mix. He's part of our plans. He's going to be a part of our success or failure as we go forward, and we're counting on him to play some good football for us."