1) I accidentally sent a ship to a planet, can I get it back somehow?
Yes, click on the planet, you should see a list of ships on the bottom left corner, select a ship than click somewhere for it to go.
2) I built my Shipyard too far from the planet and my Transport was then built without any soldiers on board, is there a way to then load soldiers?
Sent the transport to one of your planets, than launch it.
3) I sent a ship to the Shipyard, and I couldn't get it back either. Did I mis-interpret the instructions? Can I get it back...and how?
Same thing as question 1.
Hope this helps.