I think as people have been saying, heroics and flashpoints need to be different. Aside from having a different purpose/story significance (which can be debated), in general flashpoints take a lot longer. So people who don't realize a particular heroic is a flashpoint are going to be annoyed because they have to stop halfway through for some reason.
Also, I agree that bonus missions can be annoying when it is not clear at what stage in the quest you have to do them. But I think that how they work is fine. They just need to be more clear that they disappear after completing some stage of the parent quest. The thing is, the labeling there is very clear, they are bonus, not a regular quest, the goal is that if you do a little extra on a particular quest, you get a small reward.