Spoilers! Do not read unless you've seen Season 1 Episode 19, The Only Light in the Darkness.
Eric Koenig becomes very suspicious during the interrogation of Ward.
S.H.I.E.L.D. no longer exists. The agency has been labeled a terrorist organization. So why are you here?
WARD I'm an agent. It's my duty.
I need you to give that to me again.
It's my duty.
picks up pistol
I'm gonna ask you a follow-up. Agent Ward, are you associated with Hydra?
Yes. We all are. They've infiltrated the highest levels of our organization.
Like you mean it. Are you Hydra?
I'm loyal to S.H.I.E.L.D... To Agent Coulson... And to my team.
Do you have another agenda here?
Agent Ward, why are you really here?
Skye. Came back for her. I want to spend time with her.
WARD walks off wearing a lanyard
Later it is revealed that the lanyards are actually tracking devices so that he can monitor everyone's movements around the bunker.
Does Erik actually know that Ward is most likely Hydra? There was the possibility that the lie detector had given a false positive due to the pain Ward was in, so this small chance may have left a doubt in Erik's mind preventing him from shooting Ward on the spot. Additionally, at the time, Coulson and his team considered Ward to be one of themselves, so shooting him while the two were alone would have upset the team and turned them all against Erik. Because of these reasons, did Erik Koenig issue the lanyard to Ward with the intent to track him?