You get negative temperatures because it is possible to get things that are colder than the particular mix of frozen brine Fahrenheit used to set the zero for his scale.
Scalars are allowed to have any value - including negative ones.
It just means it is not a vector: it has no direction component.
The money in your bank account is also a scalar, and that can be negative too.
You are thinking of how distance, a scalar, cannot be negative ... unless you introduce direction.
However, displacement is a vector. It's magnitude is a scalar, and it's magnitude can be negative.
We just realize that a negative displacement means you finished at a position behind where you started.
It is not the scalar property that makes distance always positive, it's the physical nature of space that does this.
As soon as you leave 1D motion, the concept should become clear ... a position coordinate can be positive or negative, it is a scalar.