I'm running this task:
{
        "taskName": "tsc watch",
        "command": "tsc -w",
        "type": "shell",
        "problemMatcher": "$tsc-watch"
}
with this tsconfig:
{
    "compileOnSave": true,
    "files": [
        "src/index.ts"
    ],
    "compilerOptions": {
        "module": "commonjs",
        "sourceMap": true,
        "outDir": "dist/"
    },
    "exclude": [
        "node_modules"
    ]
}
the file index.ts only has one line in it: 
console.log('Is it working?');
And the "problems" tab is filled with HTML related warnings from random npm modules. Why? And how do i stop it?
Edit1: 
I managed to find a hack that works, by excluding the node_modules folder from the explorer: 
/* settings.json */
{
    "files.exclude": {
        "**/node_modules": true
    }
}
However this is a hack, and i still want a proper answer..
I stumbled upon this issue as well.
The only solution I found was add the skipLibCheck option and set it to true in the compilerOptions of my tsconfig.json:
{
    "compilerOptions": {
        "skipLibCheck": true
    }
}
According to the doc, it will skip type checking of all declaration files (*.d.ts), which were the ones throwing the warnings in my case.
All you should need is a tsconfig.json with:
{
    "compilerOptions": {
        "skipLibCheck": true,
    }
}
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