If you're playing using Proportions Mod 2.x (?), and have upgraded your game from an earlier Version of Proportions Mod, some components may not be repairable, so you'd need to refit to a design that uses current components.
Also, even in unmodded, there are a few component types which intentionally can't be repaired with a mere repair component - they require a full shipyard. They are the emergency components and stellar manipulations, mainly.
The Stellar components can be repaired everywhere (a common design for such ships is with a small repair bay to allow them to repair themselves). The Emergency components (Propulsion and Supplies) do require a spaceyard, as any modded component with these abilities.