@ozaffer It looks like Autodesk has corrected the issue (Opposite flag set when freezing transforms on -1 scale) sometime post Maya 2011, though I'm not sure in what version they fixed it. Clearly you're on a new enough version that you have the fix. I tested in 2016 and I don't have the issue there either...though I…
No problem @ozaffer One thing that caught my eye was your mention of utilizing the -1 scale trick. You'll find that in using that method, once you freeze transforms you'll end up with a model that is inside out. This has to do with display settings applied at the shapenode level. You might find this link valuable:…
The previous comments are correct. You have a floating face, not edge. There are some options you can enable that will help you see degenerate faces. In Windows>Setting/Preferences>Selection : Enable Face Centers This will put a dot in the middle of faces, and can help you determine collapsed faces across your model.…