Why do I get BED features outside the sequence when I'm loading a fasta file with fai index?

Full question: 
I loaded a genome in GenomeView (after samtools faidx-ing the fasta file), and for some reason some chromosomes end with a huge piece of something that doesn't belong to them. It has a track of BED, even thought I don't have any BED file in the directory (or at all).

The most likely problem is that you accidentally loaded the fasta file AND the fasta.fai file. You do not have to load the index manually, GenomeView will treat is as a separate data source, hence the bed features popping up.

When you only load the fasta file, GenomeView will use the index for fast access, but you won't get the weird additional BED features.