Hello,
Please check the information available on Repair PDF documents. Please try repairing the PDF with gs as detailed on the previous documentation. Also please note that the PDF to be merged can't be protected (for example merging a signed document).
For further support, please send to contact[at]phpdocx.com the username or email of the user that purchased the license you are using, and a PDF sample. We'll check it.
Regards.