The subpaths are probably going the wrong direction. Select the sub-paths that aren't reversing with the white arrow and then click on the non-selected of the two "Reverse Path Direction" buttons (the two center buttons in the Attributes panel).
As larry Indicated that is the problem.
When yopu a cutting out the shapes from multiple shapes to make i appear to be one shape you use the even odd rule as opposed to the non zero winding rule.
Read about the difference in the help files.
Here look the even odd fill rule all the shapes knock out so to speak
Here the Non Zero Winding rule works differently respecting each shape as its own object.