The Belgian was sent off against Arsenal on Sunday for what was deemed a dangerous tackle, but has since had his red rescinded, a decision the Red Devils manager disagrees with
The Manchester City captain was sent off for what was ruled a dangerous tackle on Jack Wilshere, but the FA's disciplinary panel decided to clear Kompany from serving a three-match ban.
Sir Alex was reluctant to add his opinion to the ongoing debate, but believes the FA have undermined themselves by not backing the decisions of their officals.
"Anything I say in that situation will be regarded as biased, so I am not going to bother with it," he told repoters.
"But it is very unusual. It does open the door of course, but that is their [the FA's] problem."