With no unread emails on my Mac, Spark on my iPad Air2 kept showing 1 unread.
I don't use Spark on my iPhone that much, but of course I wanted to check it's counter. Spark immediately warned me of an update. After installing it, both my devices jumped to a zero counter - as should.
I suppose you are then also running the latest beta version? Are you also running iOS9.3.1?
I'm not seeing a (very) recent update in the App Store. The last one is from end of February.