negative zone volume and Total wall area by ASHRAE 90.1 definition

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Zone "Atap tambahan" is indeed fully enclosed, yet its Wall and sloped Roof surfaces all have inverted vertex sequences: they're defined clockwise (when looking at them from outside the zone), e.g.:

BuildingSurface:Detailed,
    F4A4D5,                  !- Name
    Wall,                    !- Surface Type
    Exterior Wall,           !- Construction Name
    Atap tambahan,           !- Zone Name
    Outdoors,                !- Outside Boundary Condition
    ,                        !- Outside Boundary Condition Object
    SunExposed,              !- Sun Exposure
    WindExposed,             !- Wind Exposure
    ,                        !- View Factor to Ground
    3,                       !- Number of Vertices
    8.656687477963,          !- Vertex 1 X-coordinate {m}
    9.879976463316,          !- Vertex 1 Y-coordinate {m}
    4.600000000000,          !- Vertex 1 Z-coordinate {m}
    6.456687477963,          !- Vertex 2 X-coordinate {m}
    9.879976463316,          !- Vertex 2 Y-coordinate {m}
    3.400000000000,          !- Vertex 2 Z-coordinate {m}
    6.456687477963,          !- Vertex 3 X-coordinate {m}
    12.229976463316,         !- Vertex 3 Y-coordinate {m}
    3.400000000000;          !- Vertex 3 Z-coordinate {m}

... they should be counter-clockwise, given the IDF's geometry rules:

GlobalGeometryRules,
    UpperLeftCorner,         !- Starting Vertex Position
    Counterclockwise,        !- Vertex Entry Direction
    Relative;                !- Coordinate System

Incidentally, the 2x sloped Roof surfaces (like "F4A4D5" above) are labelled as Walls. That likely triggers the 90.1 surface tilt warning.