Work done relation to potential energy I know work done is negative of change in potential energy, I.e., $W=-(∆U)$.
It means that Work done against a force (or work done on a system) increases its potential energy.
And Work done by a force (or work done by the system) decreases its potential energy.
But why this is so that an internal force (by internal force I mean that a force created under a system) will always tend to decrease the potential energy of the system while the external force increase the potential energy of the system?
 A: It is important to note, that you are totally skipping the kinetic Energy $T$ part. The total energy of a system is given by $E=T+U$.
There are several examples of systems which build up potential Energy over time.
Some examples are:


*

*The mass of a pendulum is constantly cycling the total energy between kinetic and potential energy

*Objects orbiting a center of mass are generally moving on elliptic orbits. Which are also cycling between potential and kinetic energy.

*A collision of 2 comets can give one of them enough speed to leave the solar system. Thus building up potential energy for eternity.
But your observation does have a valid point. Physical systems tend to go towards lower energy states on their own. So many states which have high potential energy (e.g. a ball on a hill) are unstable. There are several additional questions which cover this topic:


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*Why does the nature always prefer low energy and maximum entropy?

*Why does a system try to minimize potential energy?

*Why a system should be at its lowest energy state for its stability?
A: The meaning of $W=-\Delta U$ has been misinterpreted here. The OP states it as

It means that Work done against a force (or work done on a system) increases its potential energy. And Work done by a force (or work done by the system) decreases its potential energy.

This is false. What this equation means is that the work done by a conservative force is equal to the negative change in potential energy associated with that conservative force. This can easily be seen by using the definition of potential energy and work. Considering a conservative force $\mathbf F$ with associated potential energy $U$:
$$\mathbf F=-\nabla U$$
The work done by this force along some path starting at position $\mathbf{r_1}$ and ending at postion $\mathbf{r_2}$ is then given by the line integral along this path
$$W=\int_{\mathbf{r_1}\rightarrow\mathbf{r_2}}\mathbf F\cdot\text d\mathbf x=-\int_{\mathbf{r_1}\rightarrow\mathbf{r_2}}\nabla U\cdot\text d\mathbf x$$
Using the fundamental theorem of calculus we arrive at
$$W=-\left[U(\mathbf{r_2})-U(\mathbf{r_1})\right]=-\Delta U$$
Therefore, this equation is only concerned with thinking about the work done by conservative forces and how that effects the potential energy associated with those forces.
