diff --git a/src/Elastic.Markdown/IO/DocumentationSet.cs b/src/Elastic.Markdown/IO/DocumentationSet.cs
index 1d22fd6..d2ba557 100644
--- a/src/Elastic.Markdown/IO/DocumentationSet.cs
+++ b/src/Elastic.Markdown/IO/DocumentationSet.cs
@@ -64,12 +64,18 @@ public DocumentationSet(BuildContext context)
 			.ToDictionary(g => g.Key, g => g.ToArray());
 
 		var fileIndex = 0;
-		Tree = new DocumentationGroup(Configuration.TableOfContents, FlatMappedFiles, folderFiles, ref fileIndex)
+		Tree = new DocumentationGroup(Context, Configuration.TableOfContents, FlatMappedFiles, folderFiles, ref fileIndex)
 		{
 			Parent = null
 		};
 
-		MarkdownFiles = Files.OfType<MarkdownFile>().ToDictionary(i => i.NavigationIndex, i => i).ToFrozenDictionary();
+		var markdownFiles = Files.OfType<MarkdownFile>().ToArray();
+
+		var excludedChildren = markdownFiles.Where(f => f.NavigationIndex == -1).ToArray();
+		foreach (var excludedChild in excludedChildren)
+			Context.EmitError(Context.ConfigurationPath, $"{excludedChild.RelativePath} is unreachable in the TOC because one of its parents matches exclusion glob");
+
+		MarkdownFiles = markdownFiles.Where(f => f.NavigationIndex > -1).ToDictionary(i => i.NavigationIndex, i => i).ToFrozenDictionary();
 
 	}
 
diff --git a/src/Elastic.Markdown/IO/MarkdownFile.cs b/src/Elastic.Markdown/IO/MarkdownFile.cs
index cbd5224..e5ff571 100644
--- a/src/Elastic.Markdown/IO/MarkdownFile.cs
+++ b/src/Elastic.Markdown/IO/MarkdownFile.cs
@@ -61,7 +61,7 @@ public string? NavigationTitle
 	public string FileName { get; }
 	public string Url => $"{UrlPathPrefix}/{RelativePath.Replace(".md", ".html")}";
 
-	public int NavigationIndex { get; set; }
+	public int NavigationIndex { get; internal set; } = -1;
 
 	private bool _instructionsParsed;
 	private DocumentationGroup? _parent;
diff --git a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
index 0faed81..3a80550 100644
--- a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
+++ b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
@@ -2,6 +2,7 @@
 // Elasticsearch B.V licenses this file to you under the Apache 2.0 License.
 // See the LICENSE file in the project root for more information
 
+using Elastic.Markdown.Diagnostics;
 using Elastic.Markdown.IO.Configuration;
 
 namespace Elastic.Markdown.IO.Navigation;
@@ -33,16 +34,16 @@ public class DocumentationGroup
 	public int Depth { get; }
 
 	public DocumentationGroup(
+		BuildContext context,
 		IReadOnlyCollection<ITocItem> toc,
 		IDictionary<string, DocumentationFile> lookup,
 		IDictionary<string, DocumentationFile[]> folderLookup,
 		ref int fileIndex,
 		int depth = 0,
-		MarkdownFile? index = null
-	)
+		MarkdownFile? index = null)
 	{
 		Depth = depth;
-		Index = ProcessTocItems(index, toc, lookup, folderLookup, depth, ref fileIndex, out var groups, out var files, out var navigationItems);
+		Index = ProcessTocItems(context, index, toc, lookup, folderLookup, depth, ref fileIndex, out var groups, out var files, out var navigationItems);
 
 		GroupsInOrder = groups;
 		FilesInOrder = files;
@@ -55,6 +56,7 @@ public DocumentationGroup(
 	}
 
 	private MarkdownFile? ProcessTocItems(
+		BuildContext context,
 		MarkdownFile? configuredIndex,
 		IReadOnlyCollection<ITocItem> toc,
 		IDictionary<string, DocumentationFile> lookup,
@@ -73,15 +75,26 @@ public DocumentationGroup(
 		{
 			if (tocItem is FileReference file)
 			{
-				if (!lookup.TryGetValue(file.Path, out var d) || d is not MarkdownFile md)
+				if (!lookup.TryGetValue(file.Path, out var d))
+				{
+					context.EmitError(context.ConfigurationPath, $"The following file could not be located: {file.Path} it may be excluded from the build in docset.yml");
+					continue;
+				}
+				if (d is ExcludedFile excluded && excluded.RelativePath.EndsWith(".md"))
+				{
+					context.EmitError(context.ConfigurationPath, $"{excluded.RelativePath} matches exclusion glob from docset.yml yet appears in TOC");
+					continue;
+				}
+				if (d is not MarkdownFile md)
 					continue;
 
 				md.Parent = this;
-				md.NavigationIndex = ++fileIndex;
+				var navigationIndex = Interlocked.Increment(ref fileIndex);
+				md.NavigationIndex = navigationIndex;
 
 				if (file.Children.Count > 0 && d is MarkdownFile virtualIndex)
 				{
-					var group = new DocumentationGroup(file.Children, lookup, folderLookup, ref fileIndex, depth + 1, virtualIndex)
+					var group = new DocumentationGroup(context, file.Children, lookup, folderLookup, ref fileIndex, depth + 1, virtualIndex)
 					{
 						Parent = this
 					};
@@ -111,7 +124,7 @@ public DocumentationGroup(
 						.ToArray();
 				}
 
-				var group = new DocumentationGroup(children, lookup, folderLookup, ref fileIndex, depth + 1)
+				var group = new DocumentationGroup(context, children, lookup, folderLookup, ref fileIndex, depth + 1)
 				{
 					Parent = this
 				};