Selecting a product variation with term reference (Color, Size, etc...) then uploading a file ( line item field ) and pressing Add to cart results in adding the first variation in queue to cart. (The selected variation is still displayed after uploading a file.)
For example - color variations order (1. Black, 2. Blue, 3. Red): User selects "Red variation" => Uploads a file => Clicks the Add to cart button => "Black variation" is added to cart, instead of the red one.
When this is done in reverse ( 1. upload a file, then select a variation ) it works, but that way isn't convenient for customers to use.