This seems to affect both the iOS and PC versions. I’m running 1.1.1 on both platforms.
When the targeting cursor is on the top row of enemy creatures, and you press the down arrow, it will potentially jump over an empty space and select one of your own creatures. I’ve attacked my own crew on more than one occasion because of this.
When pressing down while the cursor is in the top row, the targeting cursor should always select an enemy creature in the bottom row, even if it has to move one or more spaces left or right in order to do so. Selecting your own creatures as a target should only be possible if either the cursor is already in the bottom row of enemies, or the cursor is in the top row of enemies, and there are no more creatures remaining in the bottom row.