CSV import is showing the incorrect quantity of SKUs and Products

Shopify Partner
45 3 8

I have been using CSV import to update my product catalogue and, for the most part, I feel I have a handle on it.

I recently went through our product list and weighed everything so I am now looking to update the Shopify products via CSV.

However, when I go to import, it says I have 121 products and 3,044 SKUs.
Checking using /products/count.json says I have 348 products and /variants/count.json 962 SKUs.

The csv file only has 1081 lines so I don't know how it even gets to 3,044 SKUs.

I have tested just exporting the product list and importing it and it says the same thing.
I don't want to import it in case it adds an extra 3000 skus all over the place that I then need to go through and remove.

What's going here? Is there a glitch on Shopify's end? Am I over-thinking this?


edit: just tested using the same csv with only a couple of products and it seems to work properly. Still doesn't work when I try and do all of them.