Ok actual geneticist/ evolutionary biologist here: The two numbers (30,000 and 3 million) refer to different things.

The human genome is made up of about 3 billion nucleotides, like a string with 3 billion beads on it. Each of those nucleotides can be one of 4 variants: A, T, G or C - like having 4 different colours of beads.

There's inherent variation in the genome, different people will have different variants in different orders, so everyone has a unique string of nucleotides. However, that variation is not evenly distributed. There are some positions that are "polymorphic" (variable) where at a specific position different people have different variants, and there are positions that are "fixed" where virtually every person has the same letter at that position.

When we compare two people or two individuals of the same species we compare polymorphic sites, so if you pick two random people, on average 3 million of those 3 billion nucleotides at polymorphic sites will be different from each other.

When we compare species, we compare fixed sites. Those 30,000 differences between humans and neanderthals means that there are 30,000 sites in the genome where virtually all humans have one nucleotide, and virtually all neanderthals have a different nucleotide (eg, virtually all humans have a C while virtually all neanderthals have an A).