I believe it was the second one, complete train in automatic mode that I made a blueprint of. Although to confirm, I tried creating a blueprint using each of the methods, and I observed the bug in both cases, so I can't be completely sure.

I've attached a save file to reproduce the issue, it uses editor extensions to make it easier to reproduce I hope that's ok.

How to reproduce:
- Take the blueprint and place it on each of the two longer rails, so that the locomotive lines up with the fuel inserter (on the left it should be facing ...

As the subject says, when I paste my train blueprint, the locomotive would sometimes be filled with fuel, and sometimes not, and I figured out that it is determined by whether or not the bots happen to place the cargo wagon, or the locomotive first.

I've attached a video of the issue.