The questions on Khan Academy are from legit LSATs. It’s normal to feel that one test is harder than another because there actually are differences in difficulty.
The reason you’re getting differences between the scores on Khan vs LSAC is because you’re probably using this site https://www.lsac.org/lsat/lsat-prep/practice-test/computing-your-score
This tells you scoring for just the June 2007 exam. Each exam is graded on a different curve, meaning that on harder tests you can get more questions wrong yet still score the same as an easier test where you got a few less questions wrong. So the scores you’re getting from Khan are accurate.
One of the issues you’ll run into with Khan is that you’ll soon start to see the same questions over and over again when you’re doing the activities. Like others have said, Khan is a good supplementary resource but you’ll probably need something else when you start seeing repeated questions