Those are all new battle locations for Gjoerulv's Hardcore mod; picking up Kjata, Phoenix, the 4th Corel Train car, etc. That means you probably have a Hardcore mod flevel installed but the game's scene.bin isn't from the Hardcore mod (in other words the game is being made to look up enemy formations that don't exist).
As for the random crashes, that could be from the same problem; new random battles being referenced that don't have valid data in the scene.bin. I'd recommend deleting the FF7 data folder in the Steam folder and then having the game re-install itself. That should (hopefully) provide 'clean' default files. Alternatively, if you've used the Hardcore mod installer then there might be a file in the Data/Field folder called 'flevel.bak.lgp'. This should be the default flevel; delete the file called flevel.lgp and rename the 'bak' one to flevel.lgp.
