What happened to Bobbi & Hunter? [duplicate]

Out-of-universe, "it seemed like the actors were leaving the show and the film crew just sort of smashed this scene together in a hurry and ran with it" is exactly what happened. Those two actors were being considered as leads for a spin-off series focusing on just themselves as former agents of SHIELD, so they were written off the show in time for that spin-off to get started.

Late in the game, ABC ultimately decided not to go forward with the new show, so it was cancelled. (This may mean we will see Bobbi and Hunter back on Agents of SHIELD at some point.)

In-universe, they were undercover working for SHIELD when they were caught. As good agents, they were willing to stick with their cover all the way to their death, if needed, but Coulson was not. He contacted Russia through diplomatic channels and identified them as US citizens, and talked the Russians into letting them go free. However, he was forced to disavow their being US operatives -- they were let go on the premise that they were private citizens acting on their own. That means they can no longer do clandestine work for SHIELD, because if they are caught (or even seen) again, it could cause a major incident with the Russian government. So, they agreed to resign their positions and retire.