Large office building in EnergyPlus defined as just 3 separate floors without any wall connecting them

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This is not a problem or a bug. The Floor in the middle is made of zones that have a multiplier of 10: that amounts to multiplying the floor itself by 10. (E+ doesn't have the concept of floor mulitplier like eQuest does for example).

This is done because it speeds up the calculation (and input), and it doesn't introduce much error. After all, if you were explicitly modeling these 10 floors, you'd notice that they have the same boundary conditions all around (there's no site shading in these files, and the altitude-related variations will be minimal over this height)

There is useful information atop the file. I downloaded the 1.4_7.2 (Version 1.4 of the Ref Bldg, E+ version 7.2) version zip from the link you provided and opened RefBldgLargeOfficePre1980_v1.4_7.2_2A_USA_TX_HOUSTON.idf

Line 7:

! Description:  12 story plus basement, office building.

If you go to Line 625, you'll find this zone, Core_mid:

  Zone,
    Core_mid,                !- Name
    ...
    10,                      !- Multiplier
    ...

There is also a hgh-level table for floor area and number of floors for each building type here.