Not sure which GTF2BED you were using. You can either download BED file directly from UCSC table browser or convert the GTF to BED using https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html
This issue is now fixed in CrossMap v0.3.6.
Possible fix for alt alleles mapped onto the negative strand
I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version works as you expected.