I'm seeing this unwanted behaviour eversince Unity came to Ubuntu. The Unity's Launcher randomly "steals" the endpoint for the minimizing animations from Docky. In other words, when I click on an icon in Docky to minimize a window, that window minimizes to Unity instead of Docky. That happens most of the time to all of the windows, although sometimes, also randomly, it happens that the windows minimize to Docky, but very rarely.
Here's how it looks when I minimize a window: Here's how both animations should look: