The top layer is oxidization- you likely didn’t make a complete heads cut- the heads of isomerized disty turn black readily and they will likely move to the top cause heads are lighter cause density cause heads cause distillation basics…
If you gas the jar with nitrogen or argon the discoloration will stop- or will it? Show us your data and collect it often
Edit: did someone from summit tell you to put clay in the flask and expect anything but an isomerized disty to come out?
Neutral doesn’t matter at all, clays and media’s have Lewis acid activity sites and putting literally anything in the flask is begging for isomerization