Welcome @Jeff
Very odd. You do not have a chromosome location for those observations either. Do you want to share the run so we can provide feedback about how to correct this? See → How to get faster help with your question
Or, you can try a few simple fixes to learn if those are the problem. The most obvious is the presence of # header lines in GTF files from GENCODE. You can remove those headers to see what happens first, then come back here if it wasn’t enough.
- FAQ: Working with GFF GFT GTF2 GFF3 reference annotation
- FAQ: Extended Help for Differential Expression Analysis Tools
Let’s start there, thanks! 