Remember that there are many kinds of aliens-- some of them have been orbiting their stars since your species was mewling at the gates of sentience. Those combats will end horribly, and it takes a concerted effort to develop the technology to beat it. However, those species will seldom go on the offensive.
Why don't you begin with diplomacy first next time, before going in guns a-blazing?
Post designs in the ship design forum so that the community can plug glaring design holes-- like forgetting to install the correct resolution scanners or fire controls.
Secondarily, you do know you have to assign the weapons and ammo to their respective fire controls, yes? Click the targeting icon on the system map menu, select your ship, assign the details, then copy-->race to propogate that to all vessels of that type. repeat for all ship types.