diff --git a/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs b/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
index b9785e629..399b6c0b1 100644
--- a/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
+++ b/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
@@ -98,7 +98,7 @@ private async Task FetchAndValidateCrossLinks(DiagnosticsCollector collector, st
 
 			// Todo publish all relative folders as part of the link reference
 			// That way we don't need to iterate over all links and find all permutations of their relative paths
-			foreach (var (relativeLink, _) in linkReference.Links)
+			foreach (var (relativeLink, linkMetadata) in linkReference.Links)
 			{
 				var navigationPaths = _uriResolver.ResolveToSubPaths(new Uri($"{repository}://{relativeLink}"), relativeLink);
 				foreach (var navigationPath in navigationPaths)
@@ -116,6 +116,9 @@ private async Task FetchAndValidateCrossLinks(DiagnosticsCollector collector, st
 					}
 					else
 					{
+						if (_phantoms.Count > 0 && _phantoms.Contains(new Uri($"{repository}://{navigationPath}")))
+							continue;
+
 						dictionary.Add(navigationPath, new SeenPaths
 						{
 							Repository = repository,