best way to get rid of this glitch is to turn off the percentage indicator and spend less time looking at the battery meter (unless you're under 20%, at which point you should just charge your phone anyways).
I thought I was the only one having this issue. I've noticed my 6 plus doing this as well. One minute I see it's at 61%, then 5 seconds later it goes to 59%. Not a bid deal, since I get great battery life regardless, but still a weird glitch.