Samtools/bcftools calling indels in noisy reads
It's likely that the caller is being overly sensitive to deletions, which are the most common error mode for nanopore reads, even three years later in 2021.
What I'd guess is happening is that the caller is seeing a string of consecutive 1bp deletions at high frequency, and treating these as a consensus deletion covering many more bases. Looking at the pileup calls for the surrounding bases may help to diagnose this.
My general advice to people doing variant calling with nanopore is to be suspicious of deletions, especially if they include homopolymers. That usually means trying to confirm any important variants with another technology.
Newer, more accurate, base calling models are being created all the time by ONT, so if you still have the raw FAST5 data, it might be worth it to run through the most recent base caller.