Got a save where this happens, even after restarting the application.
From the save, go straight ahead into Gate A, then up the lift. Guards don't seem to mind the player wandering about.

https://www.dropbox.com/s/9c2vd5pwuo8pox0/Saves.zip

I did not tried your save but...

-Did you contain SCP-106?
-Can you show pictures of the ignoring guards?

Same thing here (0.9.1.). I left the building through Gate A, wandered straight to the three MTF-guys and they didn't react to my presence at all. They just stand there. Same thing with the lonely guard down the stairway.
I contained Radical Larry.

Thats weird...I hope they'll fix this in 0.9.2...

Just got this on another play through, this time I did the recall procedure but didn't raise Larrys box to contain him.