It looks like the good one is both planar and also has a planar neighboring face that can nicely be filled to create the inlet face.
Try using the Fill tool on the geometry (first, and alone) to make some filled-face geometry that represents the inlet face. In doing that, you should see the problems that the neighboring geometry is introducing. Remember that Fill is only as good as the surrounding faces to the fill, since what is happening (basically) is that those faces are being all extended until they meet (or diverge, and then you have your case.) Now, knowing that you can start to ease the problem by breaking up the loop, creating helper (curve) geometry, and/or creating surfaces manually.
Perhaps the second problematic face is Close to Planar (it is really hard to tell from the picture) and you might use the Simplify tool on it?
You can always post even a small portion of your geometry if you need specific ideas.
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