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Base C in red box region is misaligned. It should align with C base in black box region. Why HISAT2 add a gap before C base?
You are not likely to get a useful answer based on a small portion of the alignment you have chosen to show here (is C on its own out there on right or is there sequence beyond that). If you feel hisat2 is not working well try a different aligner.
C is at the read terminal. I was tring to find defective RNA of an RNA virus. In the default mode, there will be many reads alignment with small anchors (<=3bps). The same alignments also appear with the --pen-cansplice 12, so the gap generated seems to not due to canonical splice sites prediction by hisat2. But with the --no-temp-splicesite option, reads alignment with small anchors were reduced significantly.