I'm not sure how you made that shape, but anyway here's a method to avoid the problem entirely.

• Draw an ellipse, Copy, Paste in Place, move to one side, select both shapes.
• Click Path > Difference
• Copy, Paste in Place, reflect, move into position.

I'm not sure how you made that shape, but anyway here's a method to avoid the problem entirely.

• Draw a filled and stroked ellipse, Copy, Paste in Place, move to one side, select both shapes.
• Click Path > Difference
• Copy, Paste in Place, reflect, move into position.