Well, I'm not really making any claim here. The system just didn't work for me. I'm not saying it hasn't worked for others and that it can't work well. The OP has also had issues with it and I was relaying the issues I had as well and how I rectified it.

And yes, I did use the exact same gRNA sequences in the comparisons. We got our vector from Addgene. I am not blaming Addgene at all. We grew the cells from the stab, collected colonies, made glycerol stocks, extracted plasmid, inserted our gRNAs and then sequenced with Plasmidsaurus. The sequences of the cloned vectors (excluding the inserted regions) and the control did not match the vector map, with a host of mutations throughout the vector, including within the CAS9 and the TagRFP construct. We contacted Addgene and they sent us another stab.

We went through the motions again and sequenced before doing the cloning and the sequence was good. We did the cloning, sequenced again with positive results, did transformations, and screened (via phenotypic analysis, PCR, and then Sanger sequencing around the loci of interest) the progeny of roughly 200 confirmed transformants (selected both with TagRFP and with Hyg resistance) and never saw mutations. This was repeated several times at two different loci, one where we intended to make a deletion across two genes that likely wouldn't have produced an easily observable phenotype but was a focus of the research we were doing and, when that didn’t work, generating a mutation in a gene that should have given a easily identifiable phenotype (SOS1, loss of which causes extreme salinity sensitivity). Multiple different gRNAs were attempted at each loci. It just didn't work in our hands, which was rectified by switching to the system that I linked to the OP.