Istanbul lcov report missing tests

I'm running mocha with istanbul, es6 and babel. When I run my npm script

"test-coverage-client": "istanbul cover .mocha \"./client/**/*.test.{jsx,js}\" -- --compilers js:babel-core/register --require setup.js ",

I see all the unit tests ran and I get the Coverage Summary, but my lcov-report index file is missing a bunch of unit tests. Any clues on what might be wrong?