I'm not sure what the problem is I'll just go through the process for refuelling, see if anything looks wrong.
First on the Economics screen F2 (also known as the Summary tab of the population and production menu), click on the body in question on the Populated systems screen on the right, on the left under fuel available there should be some number listed, if it's enough fuel for refuelling then you're set.
Next on the Task groups screen (F12) Click the name drop down box and find the task group containing your ship, On the right where it says "ships in task group" you should see your ship listed, Its fuel will be listed as a percentage which is handy but if you want to see the actual number of fuel and what capacity it has you'll need to open the individual ship details screen, which conveniently can be done by double clicking the ship in this window.
On the bottom theres a box labelled "System locations available", you should see the name of your colony if it's in the same system as your task group, note that the location of your task group is listed under it's name. Click the colony, some options should appear under the 'actions available' box, click "refuel from colony" then click "Add move", under "plotted move" it should now say "Refuel from colony Earth" or whatever the name of the colony is.
If the ship is at the same location refuelling should be instant, click 5 seconds and it'll be done, however note that if some parts you have a shipyard building ships to this task group the whole group won't move. If this is the case you get a warning in the events page (control+F3) Something like "FTG Prime mover 001 cannot load movement order as there are shipyard tasks associated with the fleet".
Now if you tell the fleet to pick fuel up from a planet with 0 fuel you get no warning, just "FTG prime mover 001 has completed orders", but if there is any fuel but not enough to fully refuel you get that warning "Refuelling of Prime mover 001 could not be completed" then "FTG prime mover 001 has completed orders", it will still however take on all the fuel that was available.
Now there are 2 other options for refuelling, one is to set a standard order for the task group, click the "Special Orders/ Organization" tab, then under Conditional Order A change the condition drop down to "fuel less than 50%" then under that change "orders" to "Refuel at colony within 4 Jumps". This should make the task group automatically go get more fuel once it gets to less that 50%, however I'm not sure how smart it is in determining which body to actually get the fuel from.
Your last option is to manually transfer fuel on the Individual Unit Details screen F6 , also known as "Ships" under the main menu bar.
Find the ship you need to refuel and click it. The ships design is displayed, you can see the fuel capacity and range here (my FTG prime mover holds 500,000) , then in the top right corner you can see the ships actual fuel under the maintenance details (0 for my ship). Now click on the Miscellaneous tab, under "Manual fuel transfer(population) you can see how much fuel the colony at the ships current location has, in the box under that type in a number, I'll use 500,000, then click "Transfer from" and you should see the Population fuel drop by 500,000 and the ships fuel go up to 500,000.
That's about it for refuelling, although another interesting thing I noticed recently was that the "refuel from task group" order only shows if you select a task group with a tanker in it, that is a design that has the tanker box ticked in the design page.
