Use BLAST Command Line Applications on combined FASTA files

Hi, I have been having some difficulties with blasts I am running on several species of fish. I have been trying to combine the FASTA files as it will make my blasts much easier but have noticied some oddities. If I run a blast on a database of two fish the results I get appear to be missing matches I get when I run a blast on the two fish as individuals. The code I used for the combined blast and individual are below and both do yield results, but it seems odd to me that there sometimes isn’t overlap with individuals when there should be.

blastn –db lamprey_zebra.fasta –query zAsic2.fasta -task blastn -outfmt 7 -max_target_seqs 100

blastn –db zebra.fasta –query zAsic2.fasta -task blastn -outfmt 7 -max_target_seqs 100).

I thought this may be an issue as I manually combined the FASTA files by converting to .txt copy and pasting and then converting back to .fa. So I tried to combined through powershell using

cat *.fa > combined.fa

As I had seen this was used to combine FASTA files by others. However, when I try to convert that into a database I get the error “Blast option error: file dbcombined.fa does not match the input format type, default input type is FASTA”. So I am currently stuck as my manually combined FASTA files are not recognizing matches that should be there and combining them another way has also hit a roadblock. Any help would be greatly appreciated! Thanks, D