The court ruled against Manning in favour of the prosecutors.
She was "acquitted of the most serious charge, that of aiding the enemy, for giving secrets to WikiLeaks" under the spionage act, which means treason.
If you want an explanation from me, they said that the fact that she stole classified documents regarding national security and gave them to wikileaks, which is foreign to U.S.A., is an act of treason.
The central point is that Manning never denied to taking those documents illegally, at the time she (was still a he) said she wanted to spark public debate on the matter.