Hello,
Maybe your documents are using the same style name to apply distinct styles? On https://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP is detailed how styles are merged.
Or the last section of the first DOCX is using a continuous type as explained on https://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP in the mergeType option:
If the mergeType equals 1 or the last section of the first document is of the "continuous" type, there may be some missalignment of absolutely positioned content in the merged document. This is due to the fact that the absolute positioned content of the second document was layed out with respect the second document page distribution that may change after the merging.
Please send to contact[at]phpdocx.com both DOCX files. We'll check them.
Regards.