What is the meaning of these misaligned reads in a sequencing run? I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image.
GACCCGGTGGGTTTTAC---ACTTAAAAACACAGTCTGTAC
GACCCTGTGGGTTTTAC---ACTTAAAAACACAGTCTGTAC
          GTTTCAC---ACTTAAAAACACAGTCTGTAC
          GGTTTAC---ACTTAAAAGCACAGTCTGTAC
CCACACTCTCCTAGCAC---ACTTAAAAACACAGTCTGTAC
CCACACTCTCCTAGCACCATACTTAAAAACACAGTCTGTAC

It basically says there are reads that share part of a sequence and part of another one. The first 4 reads are the same sequence and it's a sequence that you can effectively find in the official SARS-CoV-2 assembly but the other two reads are a mix of this one with another sequence (and both are the same mix) but with only a small (3bps) indel of difference.
The sequence of the last two reads does not appear anywhere in the official SARS-CoV-2 sequence.

What does it mean?
Are these sequencing errors?
If that is the case how is it that the same mistake is repeated with similar but not exactly the same data?
If these are real RNA sequences present in the probe, why are these not used anywhere in the final assembly and how did they arrive there?

Is there any other option that I am missing?
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.