If you have 3 colonies and your civvies have only 3 ships there is only one possible explaination: you have crippled their economy by fulfilling the demand with your ships instead of patiently waiting for them to do it for you.
Basically they may have not enough profit to build new ships. If you are lucky they still have some wealth left to recover but if it's negative it may take several years for you to correct that.
You can check their status on the admin command screen.
So what to do now?
1. Find out what ships they have, hopefully we looking at some freight.
2. Stimulate.
2a. For freighters create a series of contract from a colony to another to move some basic stuff, infrastructure, mines anything needed or not needed.
2b. For colony ships create a couple of new colonies and deliver some infrastructure only there, no colonists.
The above should allow in time to generate enough cash to the civvies that will be reinvested in new ships.
Good Luck.
