So you are getting duplications of a region? Probably is being caused by a short amplicon having enough microhomology with the rear of the primers to start extension. From the sequences you have provided it is probably being caused by your forward primer. Would need to see more of the template sequence to know for sure. From the looks of it the forward primer product is making something that is annealing to the 5 bases after your reverse product. You may find adjusting extension times might help.

PCR by site directed mutagenesis produces a nicked circular PCR product that hasn't been ligated together into a plasmid. Transformation to E.coli cells ligates the PCR product together using native E.coli DNA ligase and ATP. However, before that happens occassionally you get really unlucky and the excess of primers from the reaction gets inserted into the nicks and then the plasmid gets ligated together with the primers inserted. . Use of perfectly complementary site directed mutagenesis is not actually PCR. There is no chain reaction as the primers cannot extend over the nick. So the QuickChange site directed mutagenesis doesn't work so well. It is just linear not exponential amplification.

Use of partially overlapping primers creates a nicked circular PCR product. The PCR product remains nicked all-throughout but the primers anneal over the nick and amplify the PCR product so it is a true chain reaction amplification. This method is more likely to work because it is actually PCR, but also more susceptible to primer insertion events.

I am not quite sure but looks like either the forward primer or the reverse primer or their complement was inserted over 5 times or a mixture of all the above. One thing you can do is translate the amino acid sequence of this insertion to see what the pattern is. If the insertion is in frame your enzyme could still be active with the insertion folded away from the rest of the protein. Alphafold it, but you should probably throw away this plasmid. It would be too hard to explain how the 100 amino acid in-frame insertion protein is active.

One thing you can do to make this happen less is to use a Qiagen PCR product purification kit to remove the primers from your PCR reaction product before transformation to E.coli cells. This makes the primer insertions less likely to happen. but it still happens to me.

Also, Sanger Sequencing of plasmids is kind of obsolete. Oxford Nanopore sequencing is really good. Is that what you are using? You can use Plasmidsaurus. Just ship them your plasmid and they give you results back in like 2 days for the whole plasmid using nanopore sequencing. All of the labs in my institution use Plasmidsaurus and we love it.

https://www.plasmidsaurus.com/index/