By default, the Intel Trace Analyzer and Collector traces all of your MPI communication. So, if you're using something like pthreads in your code (and you don't make any MPI calls), you need to either use the API calls for the Intel Trace Collector or use binary instrumentation on your code via the itcinstrument command to generate the trace files.
Although, since you say that a .prot file is created, something else could be going on. To get more verbose information about what the Intel Trace Analyzer and Collector is doing, you can set the VT_VERBOSE env variable.
If you have a reproducer of this, it would be great if you could submit an Intel Premier Support issue (https://premier.intel.com).