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This is an artifact in Graphics3D rendering. While ArrayMesh is new in 10.4, you would see similar behavior if you did copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd, RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]

A different workaround, suggested by halmir is to use

ArrayMesh[arr, MeshCellStyle -> {2 -> Yellow}]

This is an artifact in Graphics3D rendering (Z-fighting) which is generally difficult to avoid when using a depth buffer. 

While ArrayMesh is new in 10.4, you would see similar behavior if you did copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd,  
   RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]

This is an artifact in Graphics3D rendering. While ArrayMesh is new in 10.4, you would see similar behavior if you did copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd, RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]

This is an artifact in Graphics3D rendering. While ArrayMesh is new in 10.4, you would see similar behavior if you did copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd, RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]

A different workaround, suggested by halmir is to use

ArrayMesh[arr, MeshCellStyle -> {2 -> Yellow}]

This is an artifact in Graphics3D rendering. While ArrayMesh is new in 10.4, you would see similar behavior if you copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd, RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]

This is an artifact in Graphics3D rendering. While ArrayMesh is new in 10.4, you would see similar behavior if you did copy and paste the result into an older version.

As a possible workaround, try

SetOptions[$FrontEnd, RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}]