My guess would be that the epoxy was not thoroughly mixed. You have to mix until your arms are ready to fall off and scrape the sides of the container and bottom as well so every molecule of resin is in contact with the hardener. If not, you can get uneven hardening or "soft spots".

The fact that those areas did harden to a degree is good and often they will catch up with the rest of the epoxy with some heat and time. Even though they might not get as solid as the rest of the batch, I think the heat and time will work. Often heat will soften epoxy so don't be alarmed when you pull off your black plastic and it's soft. The heat will allow it to fire up the hardening process as it cools a bit.