Yep, sounds like a combination of the above.
If you're using a hydrometer, it'll be calibrated to a certain temperature. The hotter the liquid, the less dense it will be, which will result in a lower gravity. If you're not measuring the liquid at that temperature the hydrometer was calibrated at, then you have to make an adjustment (there are calculators out there to allow you to do this) or cool the sample down. Also, assuming it's a glass hydrometer, be careful with putting it in hot liquids! Ignore that; just saw your follow up post

Although, I did find that when I started cooling my refrac samples down, I got much more consistent results with my hydrometer readings. Could be worth a try.
The other thing is that it seems you're basing the volume measurements from the fermenters - are they plastic? If so, you could be getting some distortion/expansion from the hot liquid that could be throwing your volumes out. If you've got a straight-sided cylindrical kettle, you can make a measuring stick to work out your volume based on the depth of the liquid.
And yes, when using the above calculations for the expected gravity, you need to take all the final liquid into account; not just what you transfer to your fermenters.
Cheers,
tallie