I can replicate your results IF I group the outer shape.
I'll guess your shape has a line at the bottom off screen that connects the left and right sides.
This to allow the shape to fill (with vectors) as it would not otherwise fill (unlike raster and toonz raster which would use the border of the canvas as a fill line).
By making the shape a different group than the line that crosses over it we break a core rule of color fill in that fills work within the same group.
There are a number of things you can do to get the fill to stop at the line: ungroup everything, use the Simply Vectors option to simplify and segmentie the vector lines, group all the lines together, etc.
The general rule of thumb however is to keep things that need to be filled with color as part of the same group.
Here's some more information about how 'layering' of groups work in Opentoonz: