As I understand it, a ship that is in base contact with a blast marker has their entire base also "count as" a blast marker, so if they are also in base contact with another ship they will take their shield down as well. This doesn't keep propagating though. If your shield is only down because your touching a base that "counts as" a blast marker you don't take down other ship's shields if they are touching your base.
During the end phase both players can roll for repairing criticals. You either roll 1 dice per remaining hit point if you are not in contact with blast markers, or half that number (rounded up) if you are in contact with a blast marker.