Problem with thickening Spherical geometry

So I have figured out how to make a pinch within my sphere and now I cannot thicken it. I tried moving the cut out ellipse further from the edge and that still didn't solve the issue. I can't figure out why and the air message that SW gives me just says "Face which failed check."

Hi there,

I am trying to contruct a sphere that has a dimple in it only on one side though. So I tried doing this with the line contructed as you can see in the first image and then I did a surface boundry. Then I thicken it so I can mirror it but then the geometry started intersecting. So then instead I added a line to make it come out to a flat edge instead, but by doing this it doesn't allow me to thicken it then. Can someone help me figure out what I am doing wrong? Because essentially I want it to have a hole to go through but yet it will be closed like the handle on a detergent bottle. Thank you