I've noticed the same issue, but keep thinking that it has got something to do with my wireless charger and maybe even the hot weather right now (as crazy as that may sound, I have experienced problems charing when it's very warm). Using a regular charger, or like right now, a Mac adapter for fast charging and all, 'solves' it; it'll charge all the way up to 100%, for both the phone and Smart Battery Case (SBC).
Bit frustrating, because over the past days I keep waking up noticing my phone is at 98% and the SBC at 80%. For now I'll stop using my wireless charger, because I am confident that it is the reason it doen't fully charge.