This is difficult issue. The trade data discrepancies can be explained but need further research. There is an example of reconciliation study between Canada - USA  - Mexico on Compilers Manuals (http://comtrade.un.org/kb/attachments/SeriesF87-GUIDa64a82f464df46f69987ce41855c6cd1.pdf). For your specific case, in general, country focuses more ...

UN Comtrade data providers are mostly National Statistics Offices which are responsible for disseminating international trade statistics.  If you can give some examples, it may be possible to explain the discrepancies.