-The disc doesn't boot up and we're relying on disc swapping and gameshark codes to view whatever content we can. This is likely causing issues in-game, though, and we might not be seeing content that should be there. It's described below. The game not starting up could be due to a security measure or copy protection on the disc, and we might be bypassing it to a certain extent.
-The music is all over the place. None are associated correctly; not playing from the start of the tracks; some maps don't play music; abruptly cutting at places and resuming at others or playing other tracks; the unused Metallic Horrific plays in one of the maps. I feel like this is neither intended nor an error with the prototype; might be related to the disc swap method we're using, the game data might not be arranged the same between retail and prototype.
-An xa music file is missing on the disc.
-No sound effects during gameplay, but might be due to swapping discs.
-FMV files missing
-Pausing the game interrupts the music. The menu text itself is pretty neat. It's orange instead of yellow and looks like it uses the 1.3D font instead of the one the retail uses which IINM is based on 1.4/1.5
-Some sprites might be different (ie requiring touching up), but it's hard to tell because most of the enemy sprites are corrupted which is very likely due to disc swapping.
-In Plug n Pray, some of the maps have text on the wall near the player at the start. They all say "V X.X" or some variation (like version 2.0).
-Ministry of Fear appears to occupy E4L5 slot, and E4L6 just doesn't load. The sentry drone at the start of Ministry of Fear is absent (correction, it's actually there but the sprite is corrupted and I didn't notice it flying away out of view the first time I played it).
-In E1L1, the theater's main lobby, the posters are actually the same as the PC version, the adult movie posters.
-Random odd difference that E1L1 has the blue keycard instead of red. Correction: it's still the "red" keycard, but this appears to be some sort of palette error. All cards and readers are blue, but the messages about the cards and required cards are correct.
-In hex editor, these texts are found:
Quirk of Nature
Hotel Motel
With Cheese
Mattfort
Mancar2
Rampage
There might be more, but I haven't tested the other levels. The prototype crashes very frequently. Some of those crashing might be related to the disc swap. We can't reach the next level after completing a given one.
This site has some pre-release material scans, including some screenshots of maps not seen in the retail game. At least one of those maps is in this prototype, possibly even mancar2.map but I haven't checked that PSM scan in a while to compare. There are total 3 cut maps, all multiplayer as there are no enemies.
I also noticed E1 has Faces of Death in slot in L7 and that arena map in L8. Maybe these are in the final version too but I first noticed these maps here when using the gameshark cheat.
I'll report back later if I find more differences, and try to get some screenshots. There is also a titlepic image file in the disc contents, uncompressed. Not sure if that's also on the retail disc. I'll link that as well soon, and also a shot of the disc's file list.
Updates:
-Uncompressed title picture file, seems to not be on the retail disc:

-Assault Trooper corpse sprite:
