With this setup I have product variation in dropdown selectors and a product image upload to each Color variant. Then I have the same images uploaded to the product gallery.
When I select all the variants, the image for that variant shows twice in the product gallery as a slider.
I think what is happening in your case is that once you select a variation, the first image in the slider + the main image is replaced with the variation image.
This was done back in 1.10.3 (if I recall correctly), to have the same effect if you have the āSliderā option enabled (custom) or if you have it disabled (WooCommerce default).
For that reason, Iām not sure if I should mark this as a bug.