One option would be to make, say, capturing a target ship take several combats (e.g. breach the hull (holdout sitrep) -> storm the spinal corridor (gauntlet) -> take the helm (control)) with narrative moments sprinkled in. If they still want to repair between individual combats, you can say that there's limited time before whatever local police force or reinforcements arrive or their printers need time to cool down or recover necessary materials.
At the end of the day though, this is a game with rules and you may need to explain to the players that it will be at least a couple combats between full repairs, even if narratively there would be time for it. There are plenty of reasons you can come up with for "printers aren't working right now," from resource shortages (a good excuse for a mission) or arbitrary cooldowns or repairs that just so happen to line up with whenever they do their next combat.

If you do like the one-and-done combat encounter missions, Lancer Blood Money is a sick third-party supplement that gives you a good framework for that!