IANAL but I believe the normal protection against self-incrimination, the 5th Amendement, was not applicable due to the plea agreement she entered and thus was held in contempt of court for remaining silent.
Since Manning had already been tried for crimes related to this investigation (and found guilty, and served time), she could not be given further jail time. And because she could not be given further jail time, the courts had decided that making her testify to the grand jury about Assange wasn’t covered by the fifth amendment right to remain silent (which really only covers compelled self incrimination).
