Hi, Christoph.
First let me say that I doubt that you are seeing a bug. Everything you described sounds pretty normal.
What is the main filter
I believe that the "main filter" is another name for the contents of the Current View->Filter->General box. In other words, it's your selections for Action, Hierarchy and Completed. I don't know, maybe it's just Action. Anyhow:
How would anything be showing that does not match the main filter?
Because of hierarchy. Suppose that you have set the hierarchy filter to show parents of items that pass the filters. So once MLO has picked out all of the tasks that pass the filter, it then adds the parent items to the view. The tasks that passed the filter will be bold. Any parents, if they also passed the filter, will also be bold. Any parents that did not pass the filter will not be bold. Note that if your action filter is "All" then everything should be bold.
How can a task be bold while an identical task is not?
If one passes the filter and the other does not. Suppose that you have set the action filter to show active tasks and you are showing parents. Create a task that will be active and will be displayed in your view. Make a duplicate task and make it a subtask to the first task. The subtask will be active but the original task is not, because a task cannot be active if it has uncompleted subtasks. But the original (parent) task will still be in the view, because it is the parent of a task that's in the view and we are showing parents. So the subtask will be bold and the identical parent will not be bold.
-Dwight