The little boxes are referred to as "tofu", meaning that the font is not available for the machine TVT is running on.
Here is an example of text with illegal character
It can also mean that the font used does not include an official Unicode behind it.
Another possibility is that something went wrong during the conversion process from the source file into a e.g. PDF file.
You can easily confirm the non existing Unicode by copying the text from the original document and paste it into a Word or Wordpad/Notepad file. You will see the same boxes with question marks appearing because there is no Unicode behind the characters.
Try the following steps to avoid illegal characters:
1. Only use fonts that contain Unicode
2. Only use Adobe or compatible software to create your source files
3. When creating PDF files use a standard conversion method like e.g. Print X3 or Print X4
Using Artwork Management Systems also can create issues as the conversion processes and compression workflows can alter the files significantly. In this case the AMS workflow should be checked.