You're probably on a Macintosh. Fujifilm apparently still doesn't understand that Apple uses a different file structure than Windows (what's it been now, 26 years?). When you download a file using a Mac or iOS device such as the iPad, there's potential for the computer or device to "touch" the filesystem and write information there. Spotlight (Apple's search system) is notorious for this, but there are plenty of different programs and services that can add files on mounted storage (true of Windows, too, but generally the file structure is different and understood by the Fujifilm firmware).
Short answer: lock your card before mounting it on an Apple-based system, and then nothing will ever get written to it that the X-Pro1's firmware will have trouble understanding.
The interesting thing is that the X-Pro1 tries to read NTFS files, but fails and then just decides to go about it's own business. No error message, no shutdown, just a long delay while it tries to parse a file it doesn't understand and then gives up.
Bottom line: this is a Fujifilm problem and needs to be addressed in updated firmware. They'll say that it's an Apple problem because technically Apple doesn't follow DCF. But why should they? DCF was an attempt by the Japanese camera companies to force a standard for camera media, but they also were trying to force it on pre-existing operating systems that had moved from the old 8.3 FAT-based definitions. The reason you can type a long file name in OS-X and Windows is because those operating systems had evolved. They can also deal with larger files and more of them than DCF. The reason why Windows supports DCF slightly better is that Windows has the legacy of 8.3 FAT inherited from MS-DOS, and Microsoft has chosen to continue to support that legacy.