In general, it is advisable to restrict the names of the FASTA files to only contain the following characters:
That being said, the tools will automatically convert other characters to an underscore, "_", to avoid problems when running the methods. If you anyway get an unexpected result, try removing any characters not listed above from the file name. Also check that your file contains sequence data in FASTA format (see the question "Which type of data can be analysed using the GoSeqIt Tools platform"). The file extension has to be either .fa, .fna, .fsa, or .fasta.