The low E being thicker should acually help you pass through it as it will distribute the forces more evenly and smoothly.
Most likely it’s due to hand position. I know that making the pick consistently be 45 degrees or more on the low E is stressful for my finger. But someone like Dave Mustaine has a grip that lets it work easily on the low E
I’ve noticed this a lot in trying to play his riffs with my natural technique vs his, he has the pick in a much better grip to glide over the strings vs mine which is more slaping them. Idk if this is your issue, but it’s definitely one I’ve encountered trying to chugg the low E constantly.
My normal picking that does get caught sometimes.
His picking that glides over the string but is uncomfortable for me atm.