Ah, okay. So at some point when learning that behavior, she must have gotten the idea that she's in the correct position when slightly backed up.
One possibility is that the spoon is tipped too much toward the puppy, and the spatial pressure from the object is causing her to back up. What happens if you hold the spoon slightly forward of your position, like a lure?
Are you using a clicker or marker? If you're also using a spoon because of the height difference, then a clicker may be hard to finagle (one reason I train my dogs with both clicker and marker words is because different versions work better for different situations, and it's handy to have both!), but if you do have a marker, then one solution would be to reward heavily for touching the spoon and stopping, then re-adding the Sit separately.
So you'd first be marking and rewarding (1) dog's position relative to yours (so you reinforce her A LOT just for stopping and standing next to you in Heel position); then separately (2) the position change from Stand to Sit. Break it up to make it clearer to your puppy what exactly you want. (Bonus: you'll have a head start on moving Stands if you decide to train those later, and that is one that a lot of people have trouble with.)
Alternatively, since the spoon target seems to be slightly confused, doing it from the ground up with a foot target may help you get more clarity.
ARCHEX TDCH Pongu the Insane, CD-C, RL1X3, RL2X3, RL3X (GSD mix, b. Apr 2010)
Crookytail the Tigerwuff, RL1, NTD (Akita mix, b. Jan 2011)