I am not able to replicate this unfortunately. The game uses Ozmoo, a very advanced Z-machine interpreter. It generally is recommended to not use the game disk for saving but using a separate disk instead. I had a chat with Fredrik about it, one of the creators of Ozmoo. He downloaded the Ghosts disk and tested it and this is what he replied.
There are 96 blocks free on the disk. A save takes 44 blocks. I tried saving two times and it worked great. The third time... not so great. The save file is broken, and if you restore it you get random weirdness. To save space, Ozmoo doesn't catch disk errors, so no error message is printed when the disk gets full. And once you've done this, you have a broken file on the disk and may want to validate the disk - this will remove the protection from the story data sectors, and the next time you save the game you'll break the disk beyond repair. You could ask them for a screenshot showing the directory of the disk.
So... rule number one would be: use a separate disk :D
Could you maybe send us a screenshot from the directory as requested by Fredrik? So we get a better understanding of what goes on.