diff --git a/gitnexus-web/src/components/CodeReferencesPanel.tsx b/gitnexus-web/src/components/CodeReferencesPanel.tsx
index b1bcd1897..89ff3026d 100644
--- a/gitnexus-web/src/components/CodeReferencesPanel.tsx
+++ b/gitnexus-web/src/components/CodeReferencesPanel.tsx
@@ -3,6 +3,7 @@ import { Code, PanelLeftClose, PanelLeft, Trash2, X, Target, FileCode, Sparkles,
 import { Prism as SyntaxHighlighter } from 'react-syntax-highlighter';
 import { vscDarkPlus } from 'react-syntax-highlighter/dist/esm/styles/prism';
 import { useAppState } from '../hooks/useAppState';
+import type { GraphNode } from '../core/graph/types';
 import { NODE_COLORS } from '../lib/constants';
 
 /** Map file extension to Prism syntax highlighter language identifier */
@@ -75,6 +76,11 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
     codeReferenceFocus,
   } = useAppState();
 
+  const nodeById = useMemo(() => {
+    if (!graph) return new Map<string, GraphNode>();
+    return new Map(graph.nodes.map(n => [n.id, n]));
+  }, [graph]);
+
   const [isCollapsed, setIsCollapsed] = useState(false);
   const [glowRefId, setGlowRefId] = useState<string | null>(null);
   const panelRef = useRef<HTMLElement | null>(null);
@@ -421,7 +427,7 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
                         const nodeId = ref.nodeId!;
                         // Sync selection + focus graph
                         if (graph) {
-                          const node = graph.nodes.find((n) => n.id === nodeId);
+                          const node = nodeById.get(nodeId);
                           if (node) setSelectedNode(node);
                         }
                         onFocusNode(nodeId);
diff --git a/gitnexus-web/src/components/GraphCanvas.tsx b/gitnexus-web/src/components/GraphCanvas.tsx
index e5afc2ce9..9585584d9 100644
--- a/gitnexus-web/src/components/GraphCanvas.tsx
+++ b/gitnexus-web/src/components/GraphCanvas.tsx
@@ -82,6 +82,17 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
     setSelectedNode(null);
   }, [setSelectedNode]);
 
+  const handleToggleAIHighlights = useCallback(() => {
+    if (isAIHighlightsEnabled) {
+      clearAIToolHighlights();
+      clearAICitationHighlights();
+      clearBlastRadius();
+      setSelectedNode(null);
+      setSigmaSelectedNode(null);
+    }
+    toggleAIHighlights();
+  }, [isAIHighlightsEnabled, clearAIToolHighlights, clearAICitationHighlights, clearBlastRadius, setSelectedNode, toggleAIHighlights]);
+
   const {
     containerRef,
     sigmaRef,
@@ -154,7 +165,8 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
 
     filterGraphByDepth(sigmaGraph, appSelectedNode?.id || null, depthFilter, visibleLabels);
     sigma.refresh();
-  }, [visibleLabels, depthFilter, appSelectedNode, sigmaRef]);
+  // eslint-disable-next-line react-hooks/exhaustive-deps -- sigmaRef identity never changes
+  }, [visibleLabels, depthFilter, appSelectedNode]);
 
   // Sync app selected node with sigma
   useEffect(() => {
@@ -312,17 +324,7 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
       {/* AI Highlights toggle - Top Right */}
       <div className="absolute top-4 right-4 z-20">
         <button
-          onClick={() => {
-            if (isAIHighlightsEnabled) {
-              // Turning off — clear AI highlights and selection (preserve user query highlights)
-              clearAIToolHighlights();
-              clearAICitationHighlights();
-              clearBlastRadius();
-              setSelectedNode(null);
-              setSigmaSelectedNode(null);
-            }
-            toggleAIHighlights();
-          }}
+          onClick={handleToggleAIHighlights}
           className={
             isAIHighlightsEnabled
               ? 'w-10 h-10 flex items-center justify-center bg-cyan-500/15 border border-cyan-400/40 rounded-lg text-cyan-200 hover:bg-cyan-500/20 hover:border-cyan-300/60 transition-colors'
diff --git a/gitnexus-web/src/components/MarkdownRenderer.tsx b/gitnexus-web/src/components/MarkdownRenderer.tsx
index 8981c5756..ce40349de 100644
--- a/gitnexus-web/src/components/MarkdownRenderer.tsx
+++ b/gitnexus-web/src/components/MarkdownRenderer.tsx
@@ -90,13 +90,13 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
         return parts.join('```');
     };
 
-    const handleLinkClick = (e: React.MouseEvent<HTMLAnchorElement>, href: string) => {
+    const handleLinkClick = React.useCallback((e: React.MouseEvent<HTMLAnchorElement>, href: string) => {
         if (href.startsWith('code-ref:') || href.startsWith('node-ref:')) {
             e.preventDefault();
             onLinkClick?.(href);
         }
         // External links open in new tab (default behavior)
-    };
+    }, [onLinkClick]);
 
     const formattedContent = React.useMemo(() => formatMarkdownForDisplay(content), [content]);
 
@@ -176,7 +176,7 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
             );
         },
         pre: ({ children }: any) => <>{children}</>,
-    }), [onLinkClick]); // Removed handleLinkClick dependency as it is defined inside component but depends on onLinkClick
+    }), [handleLinkClick]);
 
     return (
         <div className="text-text-primary text-sm">