same tool name across two MCP servers silently picks the last-loaded one.
repro in 3 lines. workaround: alias one via the config. foot-gun for anyone running > 1 server.
repro
1. install two MCP servers that both expose a tool called get_pr (e.g. github + a custom one).
2. start the cli; both servers connect.
3. call get_pr. the second server's tool runs. no warning. no disambiguation.
workaround
alias one of them in ~/.claude/config.json: tools: { "gh.get_pr": "..." }. then call gh.get_pr explicitly.
why it's a foot-gun
the more MCP servers you run, the more likely you hit this. and it fails silently. i lost an hour to it last week because i thought my custom server was just broken.
filed: anthropic-mcp issue #2841.