diff --git a/client/mergediff_test.go b/client/mergediff_test.go
index 4aa0cf39adf6..adeeeb81bc99 100644
--- a/client/mergediff_test.go
+++ b/client/mergediff_test.go
@@ -428,6 +428,33 @@ func diffOpTestCases() (tests []integration.Test) {
 			),
 		})
 
+		// Check that deleting together a file from the base and another one from a merge
+		// does not result in a crash.
+		deleteFileAfterMergeCmds := []string{
+			"rm /unmodifiedDir/deleteFile1 /unmodifiedDir/deleteFile2",
+		}
+
+		extraContent := llb.Scratch().
+			File(llb.Mkdir("/unmodifiedDir", 0755)).
+			File(llb.Mkfile("/unmodifiedDir/deleteFile2", 0644, []byte("foo")))
+
+		tests = append(tests, verifyContents{
+			name: "TestDiffDeleteFilesAfterMerge",
+			state: llb.Diff(
+				base(),
+				runShell(llb.Merge([]llb.State{
+					base(),
+					extraContent,
+				}),
+					joinCmds(
+						deleteFileAfterMergeCmds,
+					)...)),
+			contents: mergeContents(
+				apply(
+					fstest.CreateDir("/unmodifiedDir", 0755)),
+			),
+		})
+
 		// Opaque dirs should be converted to the "explicit whiteout" format, as described in the OCI image spec:
 		// https://github.com/opencontainers/image-spec/blob/main/layer.md#opaque-whiteout
 		opaqueDirCmds := []string{
diff --git a/snapshot/diffapply_unix.go b/snapshot/diffapply_unix.go
index 72395d33a668..ddba5d117f7a 100644
--- a/snapshot/diffapply_unix.go
+++ b/snapshot/diffapply_unix.go
@@ -724,7 +724,10 @@ func (d *differ) overlayChanges(ctx context.Context, handle func(context.Context
 				return errors.Errorf("unhandled stat type for %+v", srcfi)
 			}
 
-			if !srcfi.IsDir() && c.srcStat.Nlink > 1 {
+			// Changes with Delete kind may share the same inode even if they are unrelated.
+			// Skip them to avoid creating hardlinks between whiteouts as whiteouts are not
+			// always created and may leave the hardlink dangling.
+			if !srcfi.IsDir() && c.srcStat.Nlink > 1 && c.kind != fs.ChangeKindDelete {
 				if linkSubPath, ok := d.inodes[statInode(c.srcStat)]; ok {
 					c.linkSubPath = linkSubPath
 				} else {