What is the meaning of these misaligned reads in a sequencing run?
The unaligned parts of the bottom two sequences are from elsewhere in the sars-cov-2 genome if you blast them. Likely causes of this are library prep. artifacts (not terribly common, but you'll find a few cases here in there once you have millions of reads) where fragments end up ligating together or (probably more likely) rearrangements of the viral sequence. My guess would be that the latter is what occurred, given how rapidly viruses reproduce. Whether that arrangement can lead to viable viruses I don't know (that's too far out of my field).

Assemblies represent at best a snapshot of a single example of a species at a single moment in time. Actual individuals in the wild can vary quite substantially, especially when they don't need to be viable.