Actually it was done on purpose. Originally NEO was Antshares, and as the name implies each Antshare was 1 'share' of the network. Just like with regular stocks basically. A share can never be less than one share.
After the rebrand to NEO this was still held on to but it was not as obvious anymore.
There are some downsides to having NEO indivisible, but also some positives. Did you know NEO is actually more scarce than Bitcoin due to it's indivisibility? There will ever only be 100.000.000 NEO which sounds like more than 21 million Bitcoin, but that foregoes by the fact that anyone can own less than 1 Bitcoin. You might own, for example, two satoshi's. But you can not own less than one NEO. That means that there can never be more than 100.000.000 people worldwide that own a NEO, but a lot more people could own a small bit of Bitcoin.