After getting captured and getting the backpack containing my stuff, opening it puts a bugged blue ammo into my inventory. It cannot be used and when trying to drop it, instantly crashes the game. Just reached the boss and as you have to use all the weapons to get through the phases, can't get past the phase which requires using the blue ammo gun. During the fight, a pickup spawns when you run out of ammo for your weapon. This worked fine for the flamethrower, however, the blue ammo always respawns immediately (can pickup hundreds of it), because the game does not recognize the bugged clip I have in the inventory as ammo and all other ones I pick up get added to the bugged one. As I can't get rid of it in any way, can't progress through the game. Will try replaying from the previous save point...

EDIT:
Replayed the game from the start as I completely missed level 0. Luckily, the bug didn't happen again and I arrived with many more lives and supplies at the same point. Here are some theories as to why the bug happened:

1) I was completely out of ammo for the blue gun when I got captured. Possible that the game expects you to have at least one blue ammo in your inventory when you open the backpack (sort of a default item) and borks itself when it reads 0, creating a dummy item that bricks the game.

2) Earlier in the level, I tried dropping a ton of stuff from the inventory on the pressure plates other than the required objects before I figured out what to do. Could be that picking up a lot of items dropped in the exact same pixel could somehow bug it or something.

3) I saved and loaded the game on the save point before picking up the backpack and opening it. This time, I immediately ran for the backpack, opened it and only then saved.

My guess is one of the three above. Though just theories, I recommend trying to avoid doing any of the above, just to make sure.