My Fairphone developed exactly this issue after upgrading to Kola Nut 1.8 (I have now rolled back to Chenpi 1.5, which appears to have solved the problem). I noticed that when I first charged it after upgrading, the red LED changed to green when the charging indicator hit 98%, rather than 100%, and the phone was hot to the touch on both sides, towards the top end. Within half an hour the charge had dropped to around 80%, and was distinctly warm just sitting in my coat pocket.
I powered it off to let it cool down, and half an hour or so later switched it on again, and it heated up again without any usage (no calls, no internet or mobile data use). The battery charge had dropped to around 30% within 5 or 6 hours.
I realise there have been many issues raised specifically in relation to the Kola Nut OS, and that the roll-out has now been postponed, but haven’t spotted this issue other than in this post. I will be staying with 1.5 for now.