I like this question. So first off
The usual rule of thumb decides whether the quantity has a direction or not with a sign (− or +) in front.
If a quantity has a negative sign it means it has a direction, right? It means it's a vector, right?
Well, not exactly. Don't get me wrong, all vectors do have a sign ($+/-$), but that doesn't mean quantities that have a negative sign are vectors.
Want an example of a scalar with a negative magnitude? Try $-50^o C$.
We know temperatures are of course not vectors. They are scalars with no directional dependency. Instead, The negative sign here is due to our frame of reference, which we have decided to be at the freezing point of pure water, ie $0^o C$. What $-50^0C$ tells us is that our current temperature is $50^oC$ below/lesser than our frame of reference, not the direction of any sort. (interestingly, using the phrase "below $0^oC$" does indeed make it sound like it's directional) Ultimately temperature is a scalar quantity with a negative value but without any directional dependency.
Put differently "All vectors may have a negative sign, but the converse is not true. Having a negative sign is not the absolute test for vector-ness". Check if they satisfy triangular/parallelogram vector addition. (see my related answer)
There are other quantities too with negative values but no directional dependencies, most notably Potential Energy. Here we are considering our frame of reference at infinity, ie the point where the magnitude is 0 is at infinity.
Now let's move to Kinetic Energy!
If I give a value of KE without any other information (i.e the sign); physically its wrong since someone might assume an accumulation of energy whereas it could actually be the opposite.
$KE$ is always a positive quantity, as $KE=mv^2$ and both mass and v^2 are positive, the latter due to maths and the former because we are not considering anitmatter. What you may be referring to must be $\Delta KE$ which yes can be negative as it $\Delta KE=KE_2-KE_1$
A negative value of $\Delta KE$ implies that $=KE_2<KE_1$ which, yes, means that the Kinetic Energy is lost or given out. Conversely, a positive value of $\Delta KE$ indicates that $=KE_2>KE_1$ or that the Kinetic energy of magnitude $\Delta KE$ is accumulated.
Once again the negative sign appears only due to our frame of reference, which is $KE_1$ here, and nothing else.
Sorry if anything sounds incomprehensible, in my defence it was already midnight when I started typing.