What process and input data is required for a cellranger reference transcriptome?
Your problem is caused by using the transcriptome fasta file rather than the genome fasta file. You've already given it transcriptome information with genome_genes.filtered.gtf, it needs the genomic sequence to go along with that.

As an aside, your GTF filtering command is unlikely to be useful unless you have a Gencode or Ensembl GTF for human. Have a look at the gene_biotypes in your file and decide for yourself what (if anything) needs to be filtered. For example, I made a cellranger reference last night for dm3 (the old fruit fly genome) with:

cellranger mkgtf annotation.gtf genes.gtf \
    --attribute=gene_biotype:protein_coding \
    --attribute=gene_biotype:ncRNA \
    --attribute=gene_biotype:snRNA \
    --attribute=gene_biotype:snoRNA \
    --attribute=gene_biotype:pre_miRNA


That should be customized for relevance. It's quite possible that your GTF doesn't even have gene_biotype attributes, that's specific to Ensembl I think.