I did the following to reproduce the error I was experiencing while running CFLint on some of my projects.
I downloaded and used Maven to build the latest dev version of CFLint (94c9574ac0d688b247d817f5b6695cff9e9c11f5).
I ran it on this project folder (cflint -folder .), which is a simple index (pulled from one of Ray Camden's old posts: https://gist.github.com/cfjedimaster/3353562#file-gistfile1-cfm).
It uses https://github.com/russplaysguitar/underscorecf, which is a really helpful library.
The generated CFLint report file is included in the repo here.
The errors in parsing mentioned in the issue (cflint/CFLint#269) are still present.
Also of note, the severity of the errors does not appear to be getting logged correctly.