I thought they knew she was an Inhuman still, but with the time restraints and the fact she could defeat them with her abilities if they tried to grab her at the wrong time, they had Daisy contact the other Inhumans first, letting Daisy fall into a false sense of security, then they'd take her.
Fitz was a similar thing, they hadn't grabbed Jemma yet, so they had Fitz act like he wasn't an LMD to draw her into a false sense of security and grab her... but the techs had put up the detector without Fitz knowing and he got caught out.
At least, that's how it appeared to me...