Part of the issue there is that the 3D-acceleration-enabled versions of Mechwarrior 2 (and Mercenaries) were buggy as heck even at the time. (Mercenaries was even pretty buggy before they did the 3D card patch, and it only got moreso.) It really doesn't help this kind of games preservation that the games themselves could be kind of junk, from a technical standpoint.
I played a ton of Mechwarrior 2 (ATI 3D Rage Edition) - the Aptiva bundle version - and didn't notice it being buggy.... Maybe this is a later version and earlier versions were more buggy?
My own experience was with the 3D-enhanced version of Mechwarrior 2: Mercenaries, specifically. It is possible that the equivalent version for Mechwarrior 2 was more stable. It's also possible my 3D drivers of the time were the cause of the issues I had, but Mercenaries was sufficiently buggy in all sorts of other ways (even the DOS version loved to crash) that I always just blamed the game.