I think this is an add-on issue not a guide issue:
I was playing through "002_32_35_Jame_Stranglethorn_Vale" and at this one point it will refuse to remove a step, even when the step was completed or clicking the square to check it off.
Specifically "T Tiger Mastery |QID|186|M|35.8,10.7|"
I deleted that step and the next step below it then would refuse to leave, completed or not just as the one above did.
So then I looked at the step above where things were freezing from: "T Return to Corporal Kaleb |O| |QID|622|M|37.7,3.3|". Deleting that step from the guide lets the addon work as expected?
Could this be an issue with the |O| tag? Or is that step formated wrong in the guide?

Found a small logic bug with the |O| tag but I don't think it was what was causing this. I'm not really sure what was, though it could have been the logic error I just fixed. I guess we'll try pushing the version I've got and see what happens? Needs more testing.

The Zul'Drak guide does the same at the beginning. There are sections where you get one quest if you did the prereq, or you get another quest if you didn't do the prereq. If you play on one computer, then move to another computer (so you're not in the same place in the guide) you will get stuck because completed quests won't check off.

My solution was to view the current guide, scroll up to the top and start checking everything until you got back to where you were supposed to be.

The |O| also appears to be producing errors when a |L| tag is present and no quantity is given.

I think this was also fixed by my loop edit, but keep an eye on it.