Right, yeah I realized that once I kept playing the game. But it was still weird to get that pop up from warning, which made me think I messed up. Oh well, I ended up starting a new game with "Story Mode" difficulty to catch up easier, so it wasn't trivial to get back to that point. Thanks for your comments.
At the terminal after first green sheild, BD can slice it. However...Cal was muttering something during it and the slice didn't work for me. So frustrating as now the shield is still up and can't progress.
Hey relik03, dont read the other comments, because they are spoilers. But Short answer, its not a bug, just leave that area, and continue to do the story. No need to restart game.
Thanks sithstatus!
