The best way to troubleshoot why data is "missing" is to simulate the data retrieval of the report by writing a job/class that uses the same query, and apply the same filters (query ranges) as you would use for running the report.
Then you can use the AX debugger to step through the code while you process the queryRun object, and see what data is being retrieved.
You may also use SQL Server Profiler to capture the calls against the database to see what is actually retrieved compared to what you'd expect, or use the AX Trace Parser tool to capture the code execution and the query as well during report execution, then check what is going on.
If data retrieval looks correct in the query, then in some cases when fonts, boxes, or various elements which are supposed to be rendered into a PDF file might not fit on the page and wrap around, get over-layered by another element, or just not show at all. You could try to use some sort of "Print to PDF" printer driver and instead of using the AX print to file option, just send it to printer with the PDF printer selected, and see if you get different results.