Check your inventory (sidebar, bottom right) for the ship you are looking for. That may give you more information about where it went if it is not where you expect it to be. Any ship Owned by you, (or if you click the corresponding header) Commanded or Piloted by you will be listed there, along with its location (if you are authorized and able to view its location).
You may also not know where You are:
You can also contact the Owner of the ship you are own by hitting the "Contact Owner" button and they may be able to shed light on what happened during your absence.
The poster keeps saying freighter. There are only around 2 freighters that even have a docking bay and can hold another ship and those can only manage a small fighter. If you don't have a docking bay in the ship you are currently on, you can't transport ships.
To get on the other ship you go to the enter/exit room of the ship you are currently on and board the one you want to be on.