My major complaint about npm is the choice to allow version range operators on dependency declarations. We know the node.js ecosystem places a high value on composability, so using lots of tiny modules which themselves depend on lots of tiny modules is the norm. This is a problem though because range operators get used liberally everywhere, so getting reproducible builds is like winning the lottery.
There are other things I don't like about using npm: node_modules/ is big and has a lot of duplication (even with npmv3), it's pretty slow, historically it has been unstable, its still crap on Windows, etc. - but for someone who has 'ensures reproducible builds' as part of their job description, the way its modules get versioned is its worst feature.