On the deployment screen you can have just one ship shown as selected (ie. highlighted in white), a different ship showing on the left (the orders and modules sidebar) and adding/changing orders will affect both of them. Steps to reproduce:
- Click a frigate.
- Click an empty spot in the deployment area.
- Select a cruiser, but do it by dragging a box over just that ship - do not click the ship directly.
- The cruiser will now be highlighted in white but the sidebar will still show the frigate. Adding orders will add them to both ships.