Ignoring "exclude" from tsconfig.json

I’m pretty sure ts-node is ignoring the exclude option in tsconfig.json. I get no errors when using tsc directly.

tsconfig.json

{
    "compileOnSave": false,
    "compilerOptions": {
        "target": "es5",
        "allowJs": true,
        "module": "commonjs",
        "moduleResolution": "node",
        "sourceMap": true,
        "emitDecoratorMetadata": true,
        "experimentalDecorators": true,
        "removeComments": false,
        "noImplicitAny": false,
        "types": [
            "node"
        ]
    },
    "exclude": [
        "node_modules",
    ]
}

ts-node main.ts

~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:308
          throw new TSError(diagnosticList)
                ^
TSError: ⨯ Unable to compile TypeScript
node_modules/json-schema/lib/validate.js (43,10): Duplicate identifier 'validate'. (2300)
node_modules/json-schema/lib/validate.js (68,5): Duplicate identifier 'validate'. (2300)
    at getOutput (~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:308:17)
    at ~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:334:18
    at Object.compile (~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:488:17)
    at Module.m._compile (~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:392:44)
    at Module._extensions..js (module.js:565:10)
    at Object.require.extensions.(anonymous function) [as .js] (~/.nvm/versions/node/v6.7.0/lib/node_modules/ts-node/src/index.ts:395:12)
    at Module.load (module.js:473:32)
    at tryModuleLoad (module.js:432:12)
    at Function.Module._load (module.js:424:3)
    at Module.require (module.js:483:17)

Also I know there is a duplicate identifier error in json-schema but using tsc main.ts and then node main.js works correctly with no changes.