There seems to be an issue with scripted doors, specifically the part in level 2 of Doom where the doors open after you killed all monsters in a room. You can't kill the monsters, so the doors don't open. No way to finish the level.
What do you mean by level 2 of Doom - E1M2? The time-delayed door reopen in E1M6? Something else? In vanilla Doom maps the only things that open when monsters die are special monster-levelnum combinations like the Hell Barons in E1M8, and the Mancubi and Arachnotrons in Doom 2 MAP07. Mr. Friendly should handle all those just fine, as it marks every monster as dead from the start (even though they're not really).
If you find a specific spot in a specific map where a door should be opening but isn't, let me know and I'll look into it.