Claude Code CLI only shows 1 of 3 identically-configured custom MCP connectors from claude.ai account

Bug: Claude Code CLI only shows 1 of 3 identically-configured custom MCP connectors from claude.ai account

Summary

My account has three custom MCP connectors pointing at the same MCP provider (Supabase), each with a different project_ref in its URL, all created the same way via claude.ai → Settings → Connectors → Add custom connector. In claude.ai's Connectors settings page, all three show as type "Custom", scope "Individual", status "Connected" (green check) — no differences in how they were set up.

• Supabase (full read/write, no project_ref scoping)
• Supabase produção RO (?project_ref=<prod-ref>&read_only=true)
• Supabase staging (?project_ref=<staging-ref>)

Claude Desktop sees and can use all three (tools reachable under each, e.g. list_tables, execute_sql).

Claude Code CLI (claude mcp list, v2.1.241) only shows one of the three:

claude.ai Supabase produção RO: https://mcp.supabase.com/mcp - ✔ Connected
claude.ai Canva: ... - ✔ Connected
claude.ai Microsoft 365: ... - ! Needs authentication
claude.ai Vercel: ... - ✔ Connected

The other two (Supabase, Supabase staging) don't appear at all — not as "Needs authentication", not as any row. claude mcp login "Supabase staging" returns:

No MCP server named "Supabase staging". Configured servers: claude.ai Canva, claude.ai Microsoft 365, claude.ai Supabase produção RO, claude.ai Vercel

So the CLI has zero record of them, even though the account-level connector page shows all three as connected identically.

Expected behavior

All three custom connectors should either all sync to Claude Code CLI, or the CLI should indicate why 2 of the 3 aren't available (e.g. some per-surface enablement toggle, a naming collision, a limit on multiple connectors against the same MCP host). Silently showing 1 of 3 with no error/warning made this look like a config problem on my end rather than a CLI-side gap.

Workaround found

Registering the missing ones directly as local HTTP MCP servers reproduces access fine:

claude mcp add --transport http Supabase-staging "https://mcp.supabase.com/mcp?project_ref=<staging-ref>" --scope user
claude mcp login Supabase-staging

This confirms the connector/URL itself is fine — it's specifically the CLI's sync of the account's custom-connector list that's dropping 2 of 3 entries.

Environment

• Claude Code CLI 2.1.241, Windows 11
• Claude Desktop app (same account) — sees all 3 connectors fine

Possible cause (guess, not confirmed)

Maybe the CLI dedupes/filters account connectors by underlying MCP server hostname (mcp.supabase.com) and only keeps one when multiple custom connectors share the same base host with different query strings — that would explain why only one "Supabase-family" connector survives while others sync fine (Canva, Vercel, Microsoft 365 — each a distinct host).