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I ran into this issue when trying to use MonoGame on Linux. I'm using Monodevelop 5.4 and tested this with Mono from the current master branch in git (c09cd684b45de5345e72a7f341b3de7156c89cc2). See https://github.com/mono/MonoGame/issues/3160 for the bug report in MonoGame. There's also a description of this bug at https://plus.google.com/+flibitijibibo/posts/KzeuHnQt96E.
MonoGame builds and runs correctly with Mono 2.10.
It appears that the name of an embedded resource is being set to the root namespace of the project plus the name of the file, without including any subdirectories.
For example, the resource named "Microsoft.Xna.Framework.Graphics.Effect.Resources.SpriteEffect.ogl.mgfxo" is part of a project with a root namespace of "Microsoft.Xna.Framework", and is located at "Graphics/Effect/Resources/SpriteEffect.ogl.mgfxo". But the assembly has the name set to "Microsoft.Xna.Framework.SpriteEffect.ogl.mgfxo".
Strangely, this issue isn't produced consistently. Some builds work fine, but other times the builds have this error. I've tried to construct a minimal example that demonstrates this behaviour and failed. For my minimal example, the embedded resource name was always correct and included the subdirectories. So it appears that there's something extra in MonoGame that triggers this issue.
I seen similar behavior for the DotSpatial project at https://github.com/DotSpatial/DotSpatial/blob/master/Source/DotSpatial.Projections/DeflateStreamReader.cs
what happens is a null pointer cause it searches the resource name "DotSpatial.Projections.AuthorityCodes.AuthorityCodeToProj4.ds" but from available resource names I got
watching at the project folder structure (https://github.com/DotSpatial/DotSpatial/tree/2871417c8e42b4b9d8eaa43b4df8834761c31ee6/Source/DotSpatial.Projections/AuthorityCodes) seems that the resource file
DotSpatial/Source/DotSpatial.Projections/AuthorityCodes/AuthorityCodeToProj4.ds was embedded w/out considering the "AuthorityCodes" subfolder in the fullname of the resource itself.
We deprecated xbuild and recommend using msbuild instead. Switching to msbuild will also most likely resolve the issue you reported.