Academic breach revealed too late Do you know if is has already happened (since 1980), that someone (academic or not) has "broken" (even in a weak sense) some cryptographic assumption, but has chosen to not first publish and directly attack some security system of the physical world?

I'm really considering the cryptographic/algorithmic level, not a human mistake in which someone didn't use the appropriate standard according to the academic world.

ps: I'm not asking about exploits which are still unknown (it would be an absurd query)
In 2004, Xiaoyun Wang's team first publicly reported collisions in MD5, and in 2007, Marc Stevens, Arjen Lenstra, and Benne de Weger reported a chosen-prefix collision attack on MD5.

Around the same time, the governments of the United States and Israel developed the the Flame malware to sabotage Iran's nuclear program.  Part of the scheme involved forging a Microsoft code-signing certificate using MD5 so that they could sign malicious software without leaving a trail pointing back to themselves.

While studying Flame in 2012, Marc Stevens discovered that the creators of Flame had used an independently developed chosen-prefix attack on MD5 (paywall-free preprint).  We can presume it is independent because if the creators knew about the attack devised by Stevens' group, why would they bother to develop a different way to do the same thing?