I know this is a bit vague but it might be a known issue:-
Sometimes when applying an Xsl document (with Aspose.pdf tags) to some Xml data the resulting pdf has overwriting where it seems as part of the output has been layered over a previous part of the output (i.e. using the Select tool each element can be selected independently). The overwriting persists on printing.
Unfortunately I cannot send the example (the information is confidential) but can you suggest where to start looking for a possible cause. The XML is produced intially via textboxes in an ASP.NET application. It has also happened when the text has been created by pasting from MSWord so might contain some special mark-up characters.