8 meters
That's not nearly enough for ten stories, unless there's some unmentioned spatial anomaly going on here. The later line "External measurements of SCP-2940 also show that only two floors are present from the outside." explains the height discrepancy, but you might want to mention it sooner. Also, what do you mean "from the outside"? You can't really see the floors when you're outside this thing, because underground.
a watch left within Floor 1 can be found in Floor 3, measuring the passage of approximately 92 days.
This makes it sound like you can leave a watch on floor 1, go to floor 3, and see the passage of time. Things like this may be why people are so confused by this article.
Time-measuring devices are inoperative
Which kind of undoes your example above.
SCP-2940-A refers to all human individuals and families residing within SCP-2940, which includes twenty-three persons.
You've already introduced the -A's as "families of three to five (each referred to as Group A through E)", which is confusing.
SCP-2940-B's skull is capable of luminescence and incandescence, presumably through a non-biological process.
The part after the comma really isn't necessary.
The majority of SCP-2940-B is composed of a male human corpse.
You've already told us this with "SCP-2940-B is a human cadaver". Some combining would be in order. It might also be a good idea to describe the lacerations and so forth before the avian parts (suggestion: "The cranium has been replaced with a fleshless skull, identified as Falco rusticolus, and both arms have wings extending from the Humerus. The plumage is also identifiable as that of Falco rusticolus.") because that makes a natural progression from least strange to most strange. Also, it would remove the physical description from the paragraph describing behavior.
SCP-2940-B displays increasing hostility towards living organisms following each floor of SCP-2940
I think a better way to phrase this would be "SCP-2940-B displays increasing hostility towards living organisms, correlated to its depth within SCP-2940". The "following each floor" phrase doesn't really make any sense, and might be another thing confusing people.
Also, it occurs to me that there's no reason for the Foundation to be treating this as one entity spread across multiple places. Why isn't it described as 10 identical entities, with increasing hostility, etc.? You could almost interpret this as literally just one entity that somehow follows Foundation personnel, teleports between floors or something, and gets more hostile the further down they are because reasons.
The description of how it kills people really isn't all that interesting, and may be a good place to cut a lot of wordiness. We can just sort of assume "big freaky dead bird man kills dudes good", unless those descriptions are really important somehow.
degenerate
This is not the right word. How about "75% (or whatever percentage you want to use, even black boxes; actually, why isn't it all of them?) of subjects' remains will convert to 12 liters of the substance exuded by SCP-2940-B."
Again, unless the description is important, how it consumes the stuff can be cut.
Masculine weeping
This strikes me oddly. Why not just 'weeping'?
Also, if they can't get to floor 9, how do they get to floor 10?
Brother is now missing from Group E, Living room is in noticeable disarray.
Either change the comma to a period, or uncapitalize "Living".
Floor 10 contains several apparatus
apparatuses
I think the water finally got to them, but at least they're all breathing.
Doesn't make sense, where's the logical connection between these phrases?
Dangit, now you've got -B going between floors, it sounds like it can always do this.
Small quantities of smoke are emitted from the doorway,
This isn't phrased quite right. Is this emitting from Floor 7's doorway? If so, you should take the last sentence of the previous paragraph and put it before this, so the connection is more clear.
it is unknown if the regenerative properties of said substance incorrectly regenerates all affected instances.
Take out "regenerative", it's redundant.