Mac Mini’ s over heat problem has been known for a while. Though the chassis is metallic, the components are closely packed and ventilation fan is small, over 90°C is quite common when
processing graphics or encoding video files. My case was that the Mac Mini (mid 2011) would hang after CPU over-heating for a while even boosting the internal fan speed to over 5000rpm. Worst situation is not bootable for a while.
Instead of placing the chassis horizontally, place it on a HK$65 metallic-like stand slightly tilted. Now on average CPU temperature is around 40°C even the fan speed is less than 3000 rpm, and around 70°C on heavy loading.
Mac Mini: Quad-core 2GHz i7 CPU, 256GB SSD
There are many stands suitable for this task, but many of them are more expensive than this stand.