You build them in a system's starbase not at the shipyard.

Where? I can't find any place on any starbase to build any civilian ships.

Originally posted by Kashim27:

Where? I can't find any place on any starbase to build any civilian ships.

In the shipyard, check your capital's starbase, third tab on the bottom of its window

Starbase does not have any shipyard. That's the message I get when I hover over the button on my capital's starbase. And this is as the Mandalorians. I also noticed all the ai empires have only one of each ship except colony ship.

Are you running any mods other than ours?

Yes. It's Stellaris of course I run mods. Let me check the list. Do any of these effect it?
BetterCheats
Better Naval Capacity
Better Starbases
Improved Space Battles [Balance]2.8
UI Overhaul Dynamic
100% Cohesion
(-United Sci-Fi Races: Robots-)
Downscaled Ships
Filthy Casual Mode
Bigger Storage Unit
UI Overhaul Dynamic-Extended Topbar
British Music
Amazing Space Battles
UI Overhaul 1080p Plus
United Fleet Shipset
Admiral Level Skills
Animated Syntheics Portraits Expanded: Reborn
Expanded Colours[180 Colours]
Expanded Stellaris Ascension Perks
Faster Ships Experience[2.8]
More Civic Points
72 Ascension Perk Slots
UI Overhaul Dynamic+Expanded Colours
Enigmatic Fortress Fix 2.6-2.8
Kath's Detailed Diplomacy
Ascension Science
Gallant Char
SW: Fallen Republic
Fallen Republic (0.9.3): Unofficial Asset Re-Scale
Proactive and Mobilised AI
Starbase Buildings & Modules
Residential Arcologies
At War: Planetary Defense Fleets 2.8 update
SW: Fallen Republic-Advisor
At War: Planetary Cannons 2.8.1 update
At war: Advanced Ship Sections 2.8.1 update
At War: Improvemetns 2.8.1 update
At War: More Patrol Craft Addon
At War: Better Admiral Experience 2.8.1 update
At War: Starbase Improvements 2.8.1 update
At War: Defense Platform Longevity 2.8.1 update
BSW//Fighter & Bomber//AVW
BSW Compatibility// At War: Starbase Improvement 2.8.1 update
Stellaris- Vaporwave Mod
Stellaris- Vaporwave Mod
Stellaris- Vaporwave Music

That would explain it, this is a total conversion mod; all of the technical aspects are already handled by the main mod, SW: Fallen Republic. The minute you add another mod that changes something on a technical level, you're going to run into conflicts.

The only other mods we suggest using are the ones in our submod collection. While it is not advised, you could probably get away with client-side mods such as music and advisors; everything else would run into problems somewhere, if not actively breaking the mod, then disrupting intended play.

If I had to guess, all of these are creating problems:
Better Naval Capacity
Better Starbases
Improved Space Battles [Balance]2.8
UI Overhaul Dynamic
100% Cohesion
(-United Sci-Fi Races: Robots-)
Downscaled Ships
Filthy Casual Mode
Bigger Storage Unit
UI Overhaul Dynamic-Extended Topbar
Amazing Space Battles
UI Overhaul 1080p Plus
United Fleet Shipset
Admiral Level Skills
Animated Syntheics Portraits Expanded: Reborn
Expanded Colours[180 Colours]
Expanded Stellaris Ascension Perks
Faster Ships Experience[2.8]
More Civic Points
72 Ascension Perk Slots
UI Overhaul Dynamic+Expanded Colours
Enigmatic Fortress Fix 2.6-2.8
Kath's Detailed Diplomacy
Ascension Science
Gallant Char
Proactive and Mobilised AI
Starbase Buildings & Modules
Residential Arcologies
At War: Planetary Defense Fleets 2.8 update
At War: Planetary Cannons 2.8.1 update
At war: Advanced Ship Sections 2.8.1 update
At War: Improvemetns 2.8.1 update
At War: More Patrol Craft Addon
At War: Better Admiral Experience 2.8.1 update
At War: Starbase Improvements 2.8.1 update
At War: Defense Platform Longevity 2.8.1 update
BSW//Fighter & Bomber//AVW
BSW Compatibility// At War: Starbase Improvement 2.8.1 update

Not only that, most of them are entirely unnecessary as our mod already does most of these things by itself.

Good to know!