Most smaller shops use some well-known third party to handle the payments, and you can tell as you are redirected to their site when it’s time to enter your card details. Some even use Amazon Pay if that’s the only one you trust.

I had a similar thing in Xcom 2 (the only one I’ve played) where I kept getting alerts that I needed more relay stations to contact the resistance, or something like that. Assuming these relays were on the ground, I kept doing missions hoping to find some. Eventually I found out I needed to clear rooms in my spaceship and build them myself. By that time I was seriously behind however.