Not a DOS game, but one of the early Prince of Persia (circa 2007) had an evil DRM trick: after a few hours into the game, there is a pressure pad activated door that does not work on cracked versions. So if you are in a cracked versions, and if the crack is not good enough, you will spend a lot of time frustrated unable to go past that door.
It is possible that the crack itself broke the game, but I want to believe it's some genius evil idea someone from Ubisoft came up with.
That isn't really the same situation. The 1981 "version" is a stealth game that is pretty much completely unrelated to the 1992 game except through name, inspiration and theme.
The 1992 game was able to use the wolfenstein name because the trademark had lapsed the the original company had gone backrupt. While the 1992 game was originally intented to include stealth gameplay, none of those gameplay features from the 1981 game really made it into the final version of the 1992 game.
Key here is that M.U.S.E. sold no rights to id software, did not bless the 1992 game in any way, and there were no personel in common between the two games. They can't really be considered as part of the same franchise
I loaded this up recently on Genesis and it actually blew my mind how smooth the animations were for the 'parkour', to find out it was all mo-capped and faithfully recreated into pixels. I had no idea people were doing this in the 80's.
This book [1], which is the creator's diaries from the time annotated with lots of memoir-ish details, is really really good and talks about how the motion capture came to be at length. It's also just a very enjoyable book, not to mention very physically beautiful.
I had to re-read the post because I assumed it was referring to that one up until I got to "Ubisoft". I was like, didn't that one guy Jordan something do the whole thing himself? (Including the rotoscoping of the character)
Well, in the 80's I had an Amstrad CPC, and there was a game named "Le passager du temps" ("Passenger of time") [1]. It was a text adventure game with some graphism in it. The goal was to explore the house of your uncle and find out where he was.
After a while, you found a machine and when you finally assemble everything and start it....the game stop working and loop in a "we're tired of hacking" message !
Of course, with the cracked version.
And it was clever, because
1) you tried the game and enjoyed it. And now you're frustrated and want to play it, so you might actually buy it
2) the anticopy test was late in the game, so everyone who copied it thought the copy was ok and spreaded it.
It is possible that the crack itself broke the game, but I want to believe it's some genius evil idea someone from Ubisoft came up with.