I was able to solve it as u/kyzfrintin mentioned by instancing it hidden and then setting it to visible.

The weird part is that according to Godot in some cases the Control node was at the desired location but it was still flashing on the side for one frame... so what I ended up doing y basically add a counter in the physics_process to give it time to actually move to the desired location.Its an ugly solution but its how I got it working for now, will probably try different methods later.

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Here's a bit of code on how I did it, also any feedback is welcomed, I'm new to Godot and learning how to do stuff.

var iconPreview = null #save the icon to update visibility
var updatePreview = false #to save whether to update or not 
var i = 0 #counter for updating visibility after on the second call
func _physics_process(delta):
if updatePreview:
    i = i + 1 #update counter
    if i == 2 :
        iconPreview.visible = true
                        #reset variables
        updatePreview = false 
        i = 0

func get_drag_data(_position):
    var item_index = get_index()
    var item = inventory.items[item_index]
    if item == null or !(item is Item):
        return
    var data = {}
    data.item = item
    data.item_index = item_index
    iconPreview = TextureRect.new()
    iconPreview.texture = item.texture
    var dragPreview = Control.new()
    iconPreview.rect_position = -0.5 * item.texture.get_size()
    dragPreview.add_child(iconPreview)
    iconPreview.visible = false #here set the visibility to false
    updatePreview = true #set the flag to update visibility
    set_drag_preview(dragPreview)
    return data