Thread:ADour/@comment-5448995-20160323225852/@comment-4651179-20160324004845

During Dark Reign, Tony Stark erased his mind and memories and used a backup of his mind to restart it, this backe-up was from an unspecified time prior to Civil War.

So it can be handwaved that Tony doesn't remember MJ living in the same house as him because he has a huge memory gap.