parts of topology not getting triangulation data

It seems that triangles are missing in your picture as well, since the entire inside should be green, except for the tube.
My process is as follows (i've omitted some code for readability):

//collect all free shapes and build single compound

TDF_LabelSequence frshapes;
myAssembly->GetFreeShapes(frshapes);

TopoDS_Compound totalShape;
BRep_Builder shapeBuilder;
shapeBuilder.MakeCompound(totalShape);

std::vector<TDF_Label> labelsList;

Standard_Integer length = frshapes.Length();
for (Standard_Integer i(1); i <= length; ++i) {
    const TDF_Label& label = frshapes.Value(i);
    TopoDS_Shape shape;
    myAssembly->GetShape(label, shape);
    shapeBuilder.Add(totalShape, shape);
}

//calculate tolerance based on object size

//generate mesh

BRepTools::Clean(totalShape);
BRepMesh_IncrementalMesh(totalShape, TOLERANCE, Standard_False, 0.5, Standard_True);

//iterate through labels​

for (Standard_Integer i(1); i <= length; ++i) {
    const TDF_Label& label = frshapes.Value(i);

    parseLabelChildren(label, handler, color, model, location);
}

//inside parse label children function

//check for color

if (assembly->IsAssembly(label)) {
    TDF_LabelSequence comps;
    assembly>GetComponents(label, comps);

    for (Standard_Integer i(1); i <= comps.Length(); ++i) {
        TDF_Label subLabel = comps.Value(i);
        TopLoc_Location newLoc = location;
        TopoDS_Shape shape;
        if (handlers.pAssembly->get()->GetShape(label, shape)) {
            TopLoc_Location loc = shape.Location();
            newLoc = location.Multiplied(loc);
        }

        parseLabelChildren(subLabel, handlers, color, model, newLoc);
    }
}
else if (assembly->IsComponent(label)) {
    TDF_Label refLabel;
    assembly->GetReferredShape(label, refLabel);
    TopLoc_Location newLoc = location;
    TopoDS_Shape shape;
    if (handlers.pAssembly->get()->GetShape(label, shape)) {
        TopLoc_Location loc = shape.Location();
        newLoc = location.Multiplied(loc);
    }

    parseLabelChildren(refLabel, handlers, color, model, newLoc);
}
else {
    TopoDS_Shape shape;
    if (assembly->GetShape(label, shape)) {
        if (shape.ShapeType() == TopAbs_COMPOUND) {
            parseCompound(shape, model, handlers, color, location);
        }
        else if (shape.ShapeType() == TopAbs_SOLID) {
            parseCompound(shape, model, handlers, color, location);
        }
        else if (shape.ShapeType() == TopAbs_SHELL) {
            parseSolid(shape, model, handlers, color, location);
        }
    }
}

at this point parseCompound just iteratest hrough topology looking for subshapes until i get to a shell, where I then iterate through all the faces. the process looks something like this

TopLoc_Location newLoc = location;
TopLoc_Location loc = shape.Location();
newLoc = location.Multiplied(loc);

Mesh mesh; //custom mesh object
uint32_t indexOffset(0);
TopExp_Explorer faceExplorer(shape, TopAbs_FACE);
while (faceExplorer.More()) {
    parseFace(faceExplorer.Current(), model, handlers, mesh, indexOffset, color, newLoc);
    faceExplorer.Next();
}

//parseFace function
//check for color, adjust transform, etc
TopLoc_Location catchLoc;

Handle(Poly_Triangulation) tri = BRep_Tool::Triangulation(face, catchLoc);
gp_Trsf transform = newLoc;
if (tri.IsNull() == Standard_False) {
    const TColgp_Array1OfPnt& nodes = tri->Nodes();
    gp_Pnt transformedPoint;

    //collect points
    for (auto point : nodes) {

        transformedPoint = point.Transformed(transform);
        mesh.Vertices.push_back(Point3D(transformedPoint.X(), transformedPoint.Y(), transformedPoint.Z()));
        mesh.Colors.push_back(Point3D(subColor.Red(), subColor.Green(), subColor.Blue()));
    }
//collect indices

    const Poly_Array1OfTriangle& triangles = tri->Triangles();
    const Standard_Integer triCount = tri->NbTriangles();

    Standard_Integer pointA(-1), pointB(-1), pointC(-1);
    Triangle polyTri;
    for (auto triangle : triangles) {
        triangle.Get(pointA, pointB, pointC);

        Standard_Integer trueA = pointA - 1 + indexOffset, trueB, trueC;
        if (face.Orientation() == TopAbs_REVERSED) {
            trueB = pointC - 1 + indexOffset;
            trueC = pointB - 1 + indexOffset;
        }
        else if (face.Orientation() == TopAbs_FORWARD) {
            trueB = pointB - 1 + indexOffset;
            trueC = pointC - 1 + indexOffset;
        }

        polyTri.a = trueA;
        polyTri.b = trueB;
        polyTri.c = trueC;
        mesh.Triangles.push_back(polyTri);

    }

//get normals...

}

and so on and so forth, for each shell. I've uploaded the cpp which contains all the parsing and iterating. it is a bit of a mess since I'm still messing around with stuff.