I don't think being bad at digging tunnels can explain the bottlenecks. They are way smaller than what you'd expect from inconsistent diameter due to poor digging.

Some inconsistency from poor digging can be ignored as a minor inconvenience. It is no big deal if in one section you have to duck a little. The bottlenecks on the other hand are so small that the noticeably impede progress, and some people probably could not get through them at all.

If they are not there intentionally that would be too big of an inconsistency to ignore.