This is most likely caused by an index file. If you want to have the multiple alignment visualization for a multi-fasta file, you should not have an index file.
Make sure that there is no file with the extension '.fai' with you fasta file.
If the problem persists, there may be an index file cached by GenomeView. You can remove cached index files by removing all files in the .genomeview/index folder in your home directory.
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.