These results are from using Cufflinks/Cuffdiff? There is an option to only perform the calculations on known genes from your reference annotation. If the reference annotation itself contains predicted genes, you could filter those out first before using it with analysis (tools: Select or one of the Text Manipulation tool group’s “Filter” tools).
The GTF annotation datatype is explained in this FAQ: Common datatypes explained
Note: All of the Tuxedo suite tools are considered deprecated. Consider using updated DE methods. Transcriptomics tutorials: