The courtyard information and crosshairs shouldn't be included in your gerbers, at least for the PCB fabrication. Each gerber represents some physical feature of the PCB: copper, silkscreen, board edges, etc.
When you submitted these files to Advanced Circuits (4pcb.com), it probably asked you to map out (or at least verify) which files represented which layers. You can mark these manufacturing-information layers as "Documentation/other", if I remember correctly.
Advanced Circuits' fab house isn't interested in assembling the boards (although they have recently developed a sister company that does this), so there is no need to send them crosshairs, pick-and-place files, or anything like that.
However, when you get the boards assembled (components placed and soldered), you should find out what the assembler wants. At the very least, they will need a BOM and a pick-and-place file (with x/y/rotation info). I have never presented this in the form of Gerbers, but I could imagine that some assemblers might want it that way...
In your specific case, it appears that Advanced Circuits thinks you want the crosshairs and courtyard outlines printed in either copper or silkscreen. You certainly don't want that!