The first sentence only tells us about the past - we don't know if the transactions are still happening. The second sentence tells us that six transactions still happen every year, and they only discovered this in 2019. You could also use perfect continuous in these sentences to show the repeated nature of the actions: 1) ... only six transactions had been happening every year. 2) ... only six transactions have been happening every year. This would also suggest that it had or could change in the future, which I think they would want as they say 'only' six.

Hello, Drew. In my opinion, the first sentence looks alright. If you want to mention that these transactions still happen, you can tell it this way instead of the second one: "By 2019, govt found out that only six transactions have happened every year." Have a great day :)

The second is better. Because you refer to every year you need to use happen. My suggestion without changing too much... By 2019, the government found that only 6 transactions happen every year