I believe there was a weekly points champion on the website a while back, but it appears some people may not have liked the feature and it was removed. There may have been a global leaderboard as well, but that was before my time so I'm not sure.
While I agree, the amount of mistakes is based upon the length of the verse. In another instance (John 4:26 "Jesus said to her, "I who speak to you am he""), I messed up the beginning with something like "And Jesus answered her" with some other variation of the phrase [thanks, whoever translated John in the ESV for the multitude of variations on this phrase...]. This resulted in two yellows and one red for that section. Add in a couple of keyboard errors due to my fast typing speed, and the system dropped me 19%, effectively erasing three months of work because I had a bad day on that verse. While the Ezekiel example was understandable, the John verse felt like the punishment didn't fit the crime. If that had happened in Ezekiel 36:23, which is four lines long, however, I would have gotten 98%. This is certainly not a cut on the website. You have to base progress on something, and mistakes vs. number of words makes the most sense. I'll just be more careful on the shorter verses.
You can also lose progress on a verse. For example, this one day I was sick of forgetting the last two verses of Ezekiel 18, so I missed literally every word in those last two verses in disgust. Imagine my surprise when it took away all of my progress and reset it to zero. Of course, I didn't notice this until the next day when the bubbles reappeared on a verse I had been studying for the last month. Thankfully, it did not reset my streak, however.
Actually, the percentage seems to be based upon a set time interval. For example, imagine if you are studying John 1, and your best verse John 1:1 has a refresh of two months while your worst verse John 1:20 has a refresh of one month. Once you get past a certain point, it will combine all those verses together based upon your weakest verse (John 1:20 in this example). So, when John 1 shows up in a month, when you complete John 1:1, it will only be at half of the time of when it is actually due. So, as a result, you'll only get 3% to the total. I think this is why you can get 100% on a verse and still only get 2% progress.
I am a techie person, and it happens to me too when the computer is practically idle. At first I thought it was because I type too fast, but it happens when I type slow also. I don't see it very often, so I just either let it go or refresh it depending on how long the verse is and where I am at in it.
There seems to be no rhyme or reason to it. For example, I created a verse set for James 1:5-8 and James 1:22-25, and studied them both for several days as sets. I wanted to have those four verses together, so I decided to do a "choose individual verses" option on both. On one of them, it acted like I had never seen the four verses before. On the other, it retained my learning from my previous repetitions. Either way, I'm not sure that there is a way to rectify it without delving into the code on the site. There's certainly no setting that I can see that affects it.