Different versions of Illustrator– have different presets in the "Save PDF" dialog. The PDF presets in Illustrator CS will not save the PDF to the correct document size if any artwork extends past the edge of the document size. It will include all objects, including those that are not visible, producing a PDF with excess white space. This will produce a PDF that is the incorrect size. If not caught prior to submission it will not print as intended.
For Illustrator CS2 and above it is recommended to use the "High Quality Print" preset.
Every file is different and it is not– feasible– to include all possible issues in this FAQ. It is always best to double check your PDF for size and excess white space before uploading.