Okay so I did the first one first, which was checking E4M9 on UDINO and, assuming you're talking about the two masterminds in the lava that shoot up at you near the entrance after you return, I could shoot them just fine with the BFG. See very poorly compressed video here https://files.catbox.moe/k46pvn.webm :^)
I also noticed a detail of the thing about trying to shoot the cyberdemon and hitting the caco, technically you should have hit both due to the way the gun works. If those two were the only things onscreen and only one was hit, somehow the BFG must have not seen a valid line to shoot the cyberdemon. I'd be very curious to know exactly where that happened, because I tried to find situations that could break the raycast aim check but it seemed very solid. If it turns out it's malfunctioning, I'll remove it right away until I can fix it.
Anyhow, time to see if I can make a Scythe 2 patch now.