After rigging, I found that those 4 corner things are out of place and not aligned to the model. this image below explains it. Any idea why? and how do I fix it?
Those are the 'boundary box' indicators...and basically the easiest way to fix it is to fix the part that doesn't have a properly aligned origin, in the modeling software you created it in.
I agree. Check the item in the modeler. Hexagon [which I use] does things like from time to time. Can be an invisible "whoknowswhat" that got created mysteriously in with the item. In Hexagon, the solution is to toggle on transparency, "right-click/drag to select" the entire wanted .obj group and do copy/delete/paste.