Hi Adriana,
thank you for the shared history. Collection #9 (bowtie2) has PE reads mapped to hg38. I used featureCounts with built-in gene models on this collection with no issue. As Jennifer pointed out, other collections use ref genomes not compatible with built-in models.
The procedure:
find featureCounts in history panel, click at it
change Gene annotation file to featureCounts built-in
change type of input to collection and select collection #9
change Does the input have read pairs to Yes, paired end and count them as 1 single fragment.
hit Run tool
History with completed featureCounts job
Kind regards,
Igor