It’s not just the Epic Store, the same applies for both Steam and GOG. Also @Valygar said
If you own PP base game and season pass it will not allow you to purchase the upgrade because you already have it and actually have even more (future DLCs).
Though I am not quite sure this is true. I only had the base game + the season pass on Epic and I was able to purchase the YOE update. But that is a steep price to pay for a cheap DLC. Luckily I had a coupon that was expiring, so I almost broke even.
It is just Epic Store as you cannot own Phoenix Point on Steam and GOG without all available DLC (including Living Weapons pack). The only customers excluded are pre-YOE Phoenix Point owners on Epic.
Interesing - so it seems like some inconsistant bug in the system. I don’t know what the problem is, but there seems to be a problem somewhere.