In a statement, Pai said he had "serious concerns" about Sinclair's proposed selloffs. As crafted, some of them would let Sinclair control the stations "in practice," violating the law even though its name wasn't officially attached. The Communications Act requires that the FCC send any transaction like this to a hearing to address the issues, the official added.
Sinclair hasn't commented on the FCC's move as of this writing. However, it has typically insisted that the merger was necessary to compete in the modern media landscape and isn't likely to be happy. A similar hearing was the final blow to Comcast's failed purchase of Time Warner Cable, as the companies knew it wouldn't survive scrutiny -- Sinclair probably wouldn't fare much better.
Unless Sinclair decides to stick through the process, the move might allay fears that Pai was assisting the merger. Pai met Sinclair's CEO days before receiving the FCC Chairman nomination, and loosened media consolidation rules not long after assuming his new role. While the FCC described the allegations of collusion as "absurd," many still believed Pai at least had Sinclair in mind during the deregulation process -- it certainly encouraged Sinclair to try its hand at a takeover. Whatever his motivations, he clearly wasn't willing to protect the merger from close scrutiny.