EDIT
The new EF designer (Beta 1 available here) will not try creating relationships to non-existing tables so instead of the error and empty model you will get a model where invalid entity types/sets and relationships are commented out.
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I looked at it for AdventureWorks for Sql Server 2012 but I think it is the same thing you hit for 2008R2/
The issue here is that the Production.Document table has a key that is of HierarchyId type and EF currently does not support HierarchyId type. EF ignores columns of types it does not understand when creating the model however if it does not understand a key column it will exclude the entire entity from the model. For excluded entities you should be able to find them commented out in the model when you open it with an Xml/Text editor. In this particular case this is what will see:
<EntityContainer Name="AdventureWorksModelStoreContainer" />
<!--Errors Found During Generation:
warning 6005: The data type 'hierarchyid' is currently not supported for the target .NET Framework version; the column 'DocumentNode' in table 'AdventureWorks.Production.Document' was excluded.
warning 6031: The column 'DocumentNode' on the table/view 'AdventureWorks.Production.Document' was excluded, and is a key column. The table/view has been excluded. Please fix the entity in the schema file, and uncomment.
<EntityType Name="Document">
<Property Name="DocumentLevel" Type="smallint" StoreGeneratedPattern="Computed" />
<Property Name="Title" Type="nvarchar" Nullable="false" MaxLength="50" />
<Property Name="Owner" Type="int" Nullable="false" />
<Property Name="FolderFlag" Type="bit" Nullable="false" />
<Property Name="FileName" Type="nvarchar" Nullable="false" MaxLength="400" />
<Property Name="FileExtension" Type="nvarchar" Nullable="false" MaxLength="8" />
<Property Name="Revision" Type="nchar" Nullable="false" MaxLength="5" />
<Property Name="ChangeNumber" Type="int" Nullable="false" />
<Property Name="Status" Type="tinyint" Nullable="false" />
<Property Name="DocumentSummary" Type="nvarchar(max)" />
<Property Name="Document" Type="varbinary(max)" />
<Property Name="rowguid" Type="uniqueidentifier" Nullable="false" />
<Property Name="ModifiedDate" Type="datetime" Nullable="false" />
</EntityType>-->
</Schema>
Notice this warning:
warning 6031: The column 'DocumentNode' on the table/view 'AdventureWorks.Production.Document' was excluded, and is a key column. The table/view has been excluded. Please fix the entity in the schema file, and uncomment.
Now in the AdventureWorks database the Production.Document table is referenced by Production.ProductDocument table. Since no entity for Production.Document table was created EF is unable to create the reference from Production.ProductDocument entity and hence the "Production.Document' is referenced by a relationship, but cannot be found.' error.
Since the Production.Document table cannot be really used "as is" by EF the easiest workaround is to exclude this entity when generating the model from entity - check all tables but Production.Document in the wizard and you should be good to go. EF will ignore all references to this entity since you excluded it and therefore there should be no error.
Link to a related work item on Entity Framework codeplex site