Issue Visualizing Control Data

[RomeroMatt]

Hello,
I have been attempting to optimize CUT&Tag for our cells of interest and I am currently analyzing our dataset along with running the controls found from the protocol found online: https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1?step=18

I have been running the script and been getting the same output as the protocol except for visualizing the data in IGV. I used all the same parameters for SEACR and took my output.bed file and created a bedgraph file with the following command: cut -f1-3,5 /Users/matthewa/Data/scripts/cut_tag/peakCalling/SEACR/${histName}_seacr_control.peaks.stringent.bed > /Users/matthewa/Data/scripts/cut_tag/peakCalling/SEACR/${histName}_seacr_control.peaks.stringent.bedgraph
Once putting into IGV, I get the following peaks (pasted below).

Protocol pic:

This looks different from what is in the protocol and many of my samples have simple blocks at their genomic sites (also pasted below).

Not sure exactly what I am doing wrong - I am still new to CUT&Tag/bioinformatics so it is possible that I am simply doing the wrong thing. Any insight would be great! Thanks!
-Matt