A known issue of the OT, C3_009, cuts off some of the text in the Technical Justification section of the output PDF if it is too long, even if all of the text is in a legal format. There are no fixes for this as of April 22, 2015, but one workaround is to truncate the text in the Technical Justification section so that it all fits within the box in the PDF output. Another is to add a number of carriage returns.
Additionally, the OT examines all text to make sure that the .xml output will be legal and printable. It is possible to import text into the OT that is illegally formatted, causing the OT to produce an error during an intended save, and so preventing the user from saving the file. For example, importing Splatalogue transition names triggered this in earlier cycles and may still do so in cycle 3. This can only be fixed by the user examining any imported text and reformatting it appropriately.