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From the WaPo article:

...Rogers was charged with making sure another insider breach never happened again.
Instead, in the past year and a half, officials have discovered two major compromises of sensitive hacking tools by personnel working at the NSA’s premier hacking unit: the Tailored Access Operations. One involved a Booz Allen Hamilton contractor, Harold T. Martin III, who is accused of carrying out the largest theft of classified government material. Although some of his activity took place before Rogers arrived and at other agencies, some of it — including the breach of some of the most sensitive tools — continued on Rogers’s watch, the officials said.
Martin’s alleged theft was discovered when some of the tools he is accused of stealing were mysteriously released online in August. They included computer code based on obscure software flaws that could be used to take control of firewalls and networks — what one former TAO operator called “the keys to the kingdom.”
Martin, who moved from the NSA to a job in a Defense Department acquisitions agency last year, was arrested in August. The news broke last month.
But there was a second, previously undisclosed breach of cybertools, discovered in the summer of 2015, which was also carried out by a TAO employee, one official said. That individual also has been arrested, but his case has not been made public. The individual is not believed to have shared the material with another country, the official said.
Rogers was put on notice by his two bosses — Clapper and Carter — that he had to get control of internal security and improve his leadership style. There have been persistent complaints from NSA personnel that Rogers is aloof, frequently absent and does not listen to staff input. The NSA is an intelligence agency but part of the Defense Department, hence the two overseers.