During execution, gnuplotfortran will create a temporary directory in your working directory. The name of this directory (hidden - as it starts with a .) is long and complicated and formed from the hostname, timestamp, etc. The probability that it will overwrite anything in your working directory is vanishingly small. This directory is removed as soon as the session is over. However, if there is an error in the execution (whether inside a gnuplotfortran library function) or outside, this could be left behind. In that case, you will have to remove it manually if you think it is important.
Each gnuplotfortran function returns a status value, which is an integer. In general, if there is no error in the execution, the returned status value would be either zero (flawless execution) or positive (warnings). Gnuplotfortran issues error messages with error codes which can help you locate the reason for the error.