Avijeet,
Part of the problem is likely that you have duplicate trailing edge points in your AF files.
Looking at the first station, for example, you have two upper TE points at 1.0, 0.0, 0.0 and two lower TE points at 1.0, -1.11...e-03, 0.0.
The result is that the wing Bezier surface tries to fit between two coincident points and causes a local loop as shown below. When you see artifacts like this, the AF points are almost always the culprit. You'll see them on the LE as well when there are duplicate points (not in yours) or when the LE is poorly resolved or interpolated from a bad source.
In short, these artifacts will cause all sorts of problems for the mesh generator because it uses the Bezier surface as the source, not the displayed panels you see on the screen like CompGeom.
You should remove those duplicate points in your airfoil files and try this again.
Section 1 close-up screenshot