Simone,
The debugger would internally work against transpiled JS, perhaps there is a mismatch there. As Stef stated earlier, you need to ensure the latest version of your source is built – typically having Project > Build Automatically on will take care of this.
For the file in question (or any file that you can replicate with), can you send us the source TS file, the transpiled JS file and the sourcemap file (.map)? Based on your compiler settings, the .map file may exist in the same folder as the JS file, or it may be included within the JS file’s source.
Thanks!