Here is my code for a honeycomb cell:
module hexagon(h,s,t,x){
difference(){
linear_extrude (height = h, center = false) circle (s, $fn=6, center =
true);
linear_extrude (height = h+1, center = false) translate ([0,0,-1])
circle (s-t, $fn=6, center = true);
}

}

module honeycomb (h,s,t,x){
hexagon(h,s,t,x);

outsidenodes=[
/*0*/[s,0,h+x],
/*1*/[s,0,h],
/*2*/[s/2,(s*sqrt(3))/2,h],
/*3*/[-s/2,(s*sqrt(3))/2,h],
/*4*/[-s/2,(s*sqrt(3))/2,h+x],
/*5*/[-s,0,h],
/*6*/[-s/2,-(s*sqrt(3))/2,h],
/*7*/[-s/2,-(s*sqrt(3))/2,h+x],
/*8*/[s/2,-(s*sqrt(3))/2,h],
/*9*/[0,0,h+2*x]
];
outsideface=[
[1,0,9,2],
[8,9,0,1],
[6,7,9,8],
[5,9,7,6],
[3,4,9,5],
[2,9,4,3]
];

union(){
polyhedron (outsidenodes, outsideface) hexagon(h,s,t,x);
}

union(){
scale ([1-(2*t)/(2*s),1-(2*t)/(2*s),1]) polyhedron (outsidenodes,
outsideface);
}
}

honeycomb(10,5,1,(5*sqrt(2))/4);

And here is the console output:
Compiling design (CSG Tree generation)…
Rendering Polygon Mesh using CGAL…
PolySet has nonplanar faces. Attempting alternate construction
PolySet has nonplanar faces. Attempting alternate construction
Geometries in cache: 9
Geometry cache size in bytes: 6624
CGAL Polyhedrons in cache: 4
CGAL cache size in bytes: 186912
Total rendering time: 0 hours, 0 minutes, 4 seconds
Top level object is a 3D object:
Simple: no
Vertices: 33
Halfedges: 128
Edges: 64
Halffacets: 66
Facets: 33
Volumes: 2
WARNING: Object may not be a valid 2-manifold and may need repair!
Rendering finished.

I am relatively new to this, so any input is appreciated. I am probably
missing something pretty basic. How can I merge a polyhedron to an object
created with linear_extrude. Is it something wrong with the polyhedron
itself?

Thanks in advance.