Hello,
This may be a Google issue, I have seen some formatting issues in the past with converting Docs to PDF such as this formatting issue shown here:
Google Support Post. Autocrat merges the data onto a Google doc first then implements the same method to change the Google doc into a PDF as you would by opening up your doc going to >file>download> PDF.
Can you do a test by merging one file to a doc and then convert it to a PDF by going to >file>download> PDF and see if you get the same formatting issues? Thanks!