Sure enough, she missed, and the game said she hit cover but I'm clearly flanking him. Is there a way to look at the actual dice roll results?
The hit chance for her bolt pistol was 95% btw. So apparently some cover sprang up when she aimed with her rifle, then receded when she swapped to her pistol, then sprang up again when she switched back to her rifle.

I'm going to write it off as slavjank and continue playing, the mystery will remain.