Nothing to fix because nothing is wrong. As far as AE is concerned you are still dealing with a whole layer representing the stage size in Flash. Therefore the only way to "fix" this would be to export the elements with the stage cropped to their boundaries. Other than that feel free to simply export PNGs or whatever and crop them suitably.
I hope the Adobe Developer can solve this problem because I want to animate the character with fit selection guide.
The only thing AE cares about is the position of the Anchor Point and you can change that. If you really want the Transform controls to tightly fit the imported drawing then you either have to make the stage size the same size as the drawing as Mylenium said or put each piece of your character in a separate composition that is the same size as the artwork. That's not as difficult as it sounds. Just select all the drawings you have imported in AE's Project Panel, right click and click new composition from selected, then choose New Comp from selection. Now open all of the timelines and carefully use AE's region of Interest tool in the Composition Panel just to the left of the Transparency Grid and Comp Camera at the bottom. Just outline the artwork. This Region of interest can then be used to crop the composition to exactly the size you want by selecting Crop to Region of Interest from the Composition Menu. Now use these cropped comps in your main comp, but you'll still need to put the anchor point where it needs to be to properly animate rotation, position and scale.