The question is: 日本で日本語能力試験が1年_______2回行われます。
I answered with に, however the correct answer is ごとに.
What’s the difference between these two and why aren’t they interchangeable in this situation?
To make matters more confusing, the grammar page for に even states “Timeframe + に + Number of Times”, which fits perfectly in the sentence above (Timeframe =1年_______2回=Number of Times).
Help is appreciated. 
I believe に is perfectly valid grammar there. I get that Bunpro is testing your knowledge of ごとに, but this should have been one of those cases where they go “Yes this is also correct, but try saying it differently.”
Hey 
You are completely right it is acceptable, actually, I would say that using ごとに would be less natural than using に in case of “periodにoccurences”.
Another alternative would be につき:
[Number+Counter] + につき + … + [Number2]
per, each
この割引クーポンは、一人につき牛乳3リットルまで使える。
This discount coupon can be used up to 3 liters of milk per person.
コンピューターを使ったら三時間につき一回、ストレッチをしたほうがいい。
If you use a computer, you should stretch once every three hours.
支払い1回につき、日本語能力試験を1回しか受けられない。
You can only take one Japanese Language Proficiency Test per payment.
1回のお支払いにつき、日本語能力試験を1回しか受けられない。
You can only take one Japanese Language Proficiency Test per payment.
広告:このバケットに限り、一点につきたったの１００円だよ！
Advertisement: Limited to this bucket, each product only 100 yen![100yen per product]