Here's my STAR command:

STAR --genomeDir human/GRCh38.p13_GENCODE.39_ERCC92 --readFilesIn veba_output/preprocess/31O0P_S1/output/trimmed_1.fastq.gz veba_output/preprocess/31O0P_S1/output/trimmed_2.fastq.gz --outFileNamePrefix star_output/31O0P_S1/intermediate/1__star/ --runThreadN 1 --outReadsUnmapped Fastx  --readFilesCommand zcat && samtools sort -@ 1 -T star_output/31O0P_S1/tmp/samtools_sort star_output/31O0P_S1/intermediate/1__star/Aligned.out.sam > star_output/31O0P_S1/intermediate/1__star/mapped.sorted.bam

Here's my transcript-level featureCounts:

featureCounts -a human/GRCh38.p13_GENCODE.39_ERCC92/gencode.v39.primary_assembly.annotation.ERCC92.gtf -o star_output/31O0P_S1/intermediate/2__featurecounts/featurecounts.transcripts.tsv -F GTF -g transcript_id --tmpDir star_output/31O0P_S1/tmp/featurecounts -T 1  star_output/31O0P_S1/intermediate/1__star/mapped.sorted.bam

Here's my gene-level featureCounts:

featureCounts -a human/GRCh38.p13_GENCODE.39_ERCC92/gencode.v39.primary_assembly.annotation.ERCC92.gtf -o star_output/31O0P_S1/intermediate/2__featurecounts/featurecounts.genes.tsv -F GTF -g gene_id --tmpDir star_output/31O0P_S1/tmp/featurecounts -T 1  star_output/31O0P_S1/intermediate/1__star/mapped.sorted.bam

In every case I'm getting more unique genes than transcripts which doesn't make any sense to me since transcripts are a subset of genes