Your computer might be short of power for 5 million polygons, as I can make the array on mine OK. You do have 211 unneeded vertices that you can get rid of by selecting one of them then Select -> Select Similar -> Amount of Connecting Edges, then press DEL and Dissolve Vertices

Also, your mesh doesn't look to be symmetrical so merging either creates holes, or, if the merge distance is set to 0.0, you get overlapping geometry. Here is a version of your cube that I have Mesh -> Bisected to produce the minimum unit. This can then be mirrored to generate your cube again.

Your computer might be short of power for 5 million polygons, as I can make the array on mine OK. You do have 211 unneeded vertices that you can get rid of by selecting one of them then Select -> Select Similar -> Amount of Connecting Edges, then press DEL and Dissolve Vertices

Also, your mesh doesn't look to be symmetrical so merging either creates holes, or, if the merge distance is set to 0.0, you get overlapping geometry. Here is a version of your cube that I have Mesh -> Bisected to produce the minimum unit. This can then be mirrored to generate your cube again.

PS here's an outline showing one way to make a grid of tubes with geometry nodes