The reads I see on IGV from my bam files don't match the counts I have.

[YM]

I used kallisto genomebam to perform pseudoalignment on stranded single-end and paired-end data and generated bam files. I visualized my bam files on IGV and compared them to the counts I got from kallisto/tximport and they don't match up. Sometimes my count would say 0 but I see reads on IGV or it says there are thousands of reads but I don't see anything on IGV. Has anyone else encountered this issue and resolved it?