In the start of this week I get upgrade token from step 26 of seasonal quest. So I obtained all upgrades before claiming all of seasonal challenges that give upgrade token. Today I claimed the last such challenge. Now tab "Upgrades" of War Table is constantly flashing. I addition, I decided to finish seasonal story on my warlock. At completion of step 26 I got another extra upgrade token.
The Legend Defiant Battlegrounds seem to be capable of giving extra upgrade material. So even if the War Table is fully upgraded, it will flash because of an unspent currency. I'll pass it to player support, I'm assuming it was never meant to give extra.