Many challenges use “Custom Map” as their setting. Any design saved on a given map name will be available on a Map with the same name, regardless of scenario changes. If a map is substantially smaller, you can place your ships outside your deployment zone.
Now one may think at this point "But if you move a ship out of the deployment zone, it gets removed entirely! Yes, it does.
But not if the ship is already deployed outside. Challenge 4587729 (my challenge, created as a sort of proof of concept) utilizes this, with a deployment saved from the largest possible zone size used on a much smaller deployment zone to place all of my ships outside the entire combat zone, causing enemy deployments to quite suddenly veer downward as the match begins.
I’ve had that problem too… I couldn’t figure it out for a while (Where the hell did those fighters come from?!) but once I did, I deleted all my deployment files in the map “Custom Map” and that fixed it.