It is easy enough for a user to make a mistake when creating an activity note on a company record and log this as a general note or another type that is not considered active engagement. If the user notices this and tries to update the note to have a type that is active engagement, this will not set the last active engagement on the company record again. That last active engagement is currently only set on the creation of a note if the type of that note is active engagement.
This is pretty hard to implement as so many different things can set the engagement dates.