I modified the first line to add an M or an H to distinguish in between the and it works fine with STAR (below). For some reason featurecounts doesn't recognize the files that contsain the "1M" or "1H" as GTF file even when I specify it with -F and they have a similar structure to the original file.

# modify files, mark human with H in fasta and gtf, and mouse with M. It will create new files called "human.fa" and "mouse.fa"
awk '{if ($0 ~ /^>/) {print $1 "H"} else {print $0}}' Homo_sapiens.GRCh38.dna.primary_assembly.fa > human.fa
awk '{if ($0 ~ /^>/) {print $1 "M"} else {print $0}}' Mus_musculus.GRCm39.dna.primary_assembly.fa > mouse.fa

#modify files, mark human with H in fasta and gtf, and mouse with M. it will create two new files called "human.gtf" and "mouse.gtf"
awk '{sub("$", "H", $1)}; 1' Homo_sapiens.GRCh38.113.gtf > human.gtf
awk '{sub("$", "M", $1)}; 1' Mus_musculus.GRCm39.113.gtf > mouse.gtf

#remove header, header won't matter for STAR indexing and alignment but subread and feature counts can't read the concatenated gtf with headers
grep -v "#" human.gtf > human1.gtf
grep -v "#" mouse.gtf > mouse1.gtf

# catenate gtf's in one:
cat human1.gtf mouse1.gtf > HumanMouse.gtf

Answer below. I am getting the feeling that by modifying the gtf files I might have accidentally modified the delimiter...? Maybe it is not a tab anymore? How can I change the first line in my gtf to have 1H or 1M and still maintain tab as delimiter?