I think it's because they're older/have less security features. To be fair, the last time the Bureau of Engraving and Printing issued these bills was in 1996, and that's 25 years ago, plus and the average lifespan of a $100 bill is 22.9 years.
Buyers at the cuevas refuse to accept Cara chica dollar bills, according to cueveros . Hence a 3 % penalty in the Exchange rate, it takes longer to move them. Also clients refuse Cara chica bills at the banks. Some Cara chica bills have been under the mattress since 2001, sometimes in poor condition due to humidity .Harder to detect fake bills in 1996 versions bills