I've noticed a couple of issues with the way the compiler resolves the output directory structure. I've attached a minimal project that can be used to reproduce these issues, it's setup as an NPM package, so after downloading and extracting just run npm install to install the latest nightly build of TypeScript (support for filenames in the --project compiler option was added very recently).

Issue 1

From the package root run

node ./node_modules/typescript/bin/tsc --project src/good-tsconfig.json

Note that the output directory structure is (as expected):

lib/
  first/
    file1.js
  second/
    file2.js

Now run

node ./node_modules/typescript/bin/tsc --project src/bad-tsconfig.json

Note that the output directory structure is missing the subdir second:

lib2/
  file2.js

While the expected output directory structure is:

lib2/
  second/
    file2.js

Issue 2

I'm not sure if this is a bug or just user error, but it can be reproduced starting with TypeScript 1.6.2 (and possibly earlier, that's just the oldest version I've tried). Run

node ./node_modules/typescript/bin/tsc --project src/second

Note that the output directory structure is:

lib3/
  second/
    first/
      file1.js
    second/
      file2.js

While the expected output directory structure is:

lib3/
  first/
    file1.js
  second/
    file2.js