It's mostly the transition from the first three frets on the 6th string and then making my way down each string on the same three frets.
It's difficult to press down on the first fret with my index finger in a good position because I can't stretch my middle finger to the second fret. If I do stretch my middle finger then my index finger ends up going to a sideways angle rather than pushing the string down with my fingertip, causing a clunky sound.
This happens when I hold the back of the neck in the palm of my hand with my thumb slightly resting on the top of the neck. So to compensate I move my thumb maybe to the middle back of the neck which makes it a lot easier for my fingers to hold the strings down to the neck as it gives me more room to stretch my fingers.
I just didn't know if this was a bad habit or if it was the usual, judging from the tutorial it seems to be pretty normal (I'm hoping).
Sorry if this is confusing, first time ever using the lingo :p