The answer was in the stars. For some reason, Earthlings had founded universities, and those universities had supported thousands of astronomers for hundreds of years. They refined their techniques over the centuries, collecting databases of statistics on distant stars which no human could ever visit.
And then a grad student in cryptography had gotten fed up with her adviser and switched to astronomy. To familiarize herself with the star database, Li had fed the coordinates of all the known stars in the galaxy into a PRNG test suite used to assess the predictability of cryptographic random number generators.
She hadn't been surprised when the database failed the test; stars aren't randomly distributed, and as they later found, at least 7 different astronomical techniques had also added artificial patterns to the database. However, Li thought it amusing when the test suite claimed the values were generated by a Linear Feedback Shift Register, the simplistic random number generator included in most programming libraries. It had even helpfully produced the LFSR parameters which, with a few lines of code, would generate a sequence of numbers that the test suite thought were somehow related to the database values.
Li had shown it to her advisor, and over a few months they had toyed with the results at odd hours, musing on a publication about systemic errors in sky survey techniques, or perhaps uncovering evidence of fabrication by some unscrupulous astronomer. When Li's model started predicting locations of stars before they were discovered, they worked full time on it for 18 months before telling another soul: surely it would be seen as plagiarism, not prediction.
But in the end, the systemic errors were identified and eliminated, and Li was confirmed to have made the greatest scientific discovery in all of history: the universe they lived in was incontrovertibly a simulation. And moreover, whatever Gods had placed the stars in their galaxies had been lazy in their choice of random number generators, just as human programmers are. (This did create a certain smugness among the kind of cryptographers who used cryptograpic-strength PRNGs to shuffle music playlists.)
As news-show pundits spouted absurdities and mankind came to grips with the hand of God, scientists in all fields now knew what to look for, and found bugs aplenty.
And as the fabric of the universe resolved under our microscopes, it was the cryptographers once again who made a profoundly disturbing hypothesis. The universe was made of bits, and manipulated by algorithms. Far more bits than our computers had, and running algorithms more complex than mankind had ever managed. But we knew there were bugs. What if some of those bugs were also security holes?
Teenagers had been exploiting complex systems for years. A carefully crafted string of a few hundred unexpected characters could cause a buggy subroutine to turn a user into an administrator. Or, if the string was slightly off, crash the server. This was normally no concern to the budding hackers. But then, they usually weren't hacking their own life support.
When the politicians finally understood, the strictest laws were passed. But studying really isn't much different than hacking, and eventually we learned all about our host machine. And several of the shortcomings of our universe started looking tantalizingly exploitable.