I've seen numerous off hand comments claiming that Arena doesn't implement the rules of Magic the Gathering correctly. (Here's a single example on a comment to my answer: Does a phased-out Ring-bearer stop being the Ring-bearer when the Ring tempts you?)
Every rules discussion I follow on Stack Exchange that seems counter intuitive or wrong to me, I test on Arena, and it has always been implemented correctly.
I am aware that there have been some blatently bad bugs, aside from those, are there examples where the rules were implemented incorrectly?