After coming out of 049's containment chamber, I encountered another room that I had already encountered before I went through the elevator it was a room that contained SCP-714 and SCP-1025, I picked them both up and ended up with two of the same objects I had already picked up (Keep in mind I have god mode on, because I wanted to have a quick play and see what was new):

Seems to be from dup-ing rooms. It happens a lot with the new electrical box room for some reason, and the layout is a little messed up with the sections and whatnot, they go from an office hallway to a keter hallway and it doesn't blend well. Some other rooms have too small spawn rates too. Namely the offices.

Took a quick look and found room2scps (714/1025 room) is used twice, once in zone 2 and another time in zone 3. I'm going to assume one of these is a typo (Probably 3 since 2 has 049, and the nukes in it).
In Vanilla 0.7 MapSystem.bb: I don't know which room is supposed to go where, so I'm just going to leave you guys with this to decide for yourselves.
If you want, I could look further into this to see what room is likely supposed to be in zone 3 and upload a fix.