Many on social media criticized GDAX and alleged there was some sort of illegal activity taking place. GDAX denied this.

“Our initial investigations show no indication of wrongdoing or account takeovers. We understand this event can be frustrating for our customers. Our matching engine operated as intended throughout this event and trading with advanced features like margin always carries inherent risk,” White said in a blog post.

“We are continuing to conduct a thorough investigation and will keep customers updated with any resulting actions.”

White also noted that these trades are final and will not be reversed. The exchange temporarily halted trading of ethereum on Wednesday before restoring the system shortly after.

Ethereum was trading at around $317 on the GDAX exchange in the early hours of Thursday morning. According to industry and price tracking website Coinmarketcap, which takes into account the price on several exchanges, ethereum was trading around $336.

As well as the issues on GDAX, investor demand at the funding launch for an ethereum-based messaging app called Status clogged the ethereum network, an industry insider told CNBC.

Ethereum traders were outraged by the crash blaming GDAX for not having proper controls, and even accusing whoever put the sell order in of market manipulation.

And it was a painful experience for many. On the social forum Reddit, users complained of losing large sums of money from $3,000 to $9,000.

But it also seemed to be a large money making event for some too. On the trading forum StockTwits, user John DeMasie posted a screenshot of trade history around the time of the flash crash. It showed one person had an order in for just over 3,800 ethereum if the price fell to 10 cents on the GDAX exchange. Theoretically this person would have spent $380 to buy these coins, and when the price shot up above $300 again, the trader would be sitting on over $1 million. CNBC has been unable to verify the screenshot posted by DeMasie.

The ethereum crash comes amid rising interest in the broader cryptocurrency space. Both bitcoin and ethereum have hit record highs recently, and have both seen pullbacks.

Ethereum in particular has been talked up because of the blockchain technology that underpins it. Whereas bitcoin and its blockchain is seen as a payment network, ethereum has been designed to support so-called smart contract applications. A smart contract is a computer program that can automatically execute the terms of a contract when certain conditions are met.

The ethereum blockchain has also got backing from a number of large firms such as Microsoft, which has helped to drive the price higher.

Ethereum is up around 4,100 percent year-to-date, based on the price it was trading at on Thursday morning, according to Coinmarketcap.