I think the size of the penalty is an indication that the scale of the illegal activity relative to the total trading volume on Coinbase was probably minimal.

Considering the description of how this happened (two independent trading bots that sometimes matched one another) it sounds more like a lack of controls rather than any malicious intention to deceive markets. And, at least for now, intent matters in our legal system.

it sounds like there was two things that happened:

1. What you said. Two bots that lacked controls and interacted with eachother. which may have been accidental

2. A rogue employee intentionally using those bots to fake volume on a specific currency pair. This is actually malicious.