Work and energy are in fact different things, but they are closely related. So closely that they share the same units. To understand the difference between them and why this difference does not imply new units, let me borrow a story told by Feynman in his Lectures on Physics and improved by Van Ness in his Understanding Thermodynamics.
Let us imagine a boy living in a house with his mother and 37 indestructible small cubes. The house has two windows labeled by $W$ and $Q$. Every day the mother counts the cubes and some day she finds only 35. The boy does not say where are the two missing cubes but the mother notice that they can be inside a box which (by some reason) she cannot open. She weights the box, wait until another day when she counts 37 cubes, weights the box again, takes the difference between the readings and divide it by the weight of one cube. She finds out that the two cubes missing the other day were inside the box. Another day she counts only 30 cubes. She weights the box again, does the math and notice there are still 3 cubes missing. She realizes that those missing cubes can be on the bathtub. She cannot either see or check with is hands because the water is dirty. She measure the level that day and in another day when there is no cube missing, does the math and can now account for blocks in the bathtub. She has a formula able to account for blocks eventually hidden in the box and in the bathtub:
$$37=\mathrm{visible\ cubes}+\frac{\mathrm{weight\ box}-\mathrm{weight\ empty\ box}}{\mathrm{weight\ one\ cube}}+\frac{\mathrm{level\ bathtub}-\mathrm{level\ bathtube\ with\ no\ cube}}{\mathrm{change\ of\ level\ due\ to\ one\ cube}}.$$
One day however she checks the box and the bathtub but she cannot find 37 cubes. Some day she finds even 40 cubes! The only conclusion is that there are cubes being thrown in and out the windows. She came up with another formula:
$$\mathrm{number\ cubes}-37=Q+W$$
where $Q$ and $W$ denotes the number of cubes that crosses the windows $Q$ and $W$. If the cube comes in, the number is positive, if the cube is thrown out, the number is negative.
So, the first equation is a conservation law and the 37 cubes metaphorically represents energy. The three terms on the right means different ways energy (cubes) can show up. It could represent, for instance, kinetic energy, rest mass energy, the different potential energies. All with the same units. The second equation represents a way of accounting for energy (cubes) entering and living the system (the house) via heat (window Q) or work (window W). Again, all the terms in that equation has the same units. That formula actually represents the first law of thermodynamics and $W$ stands for work. As you can see, work is the term given for energy that enters or leaves the system in a given way (window W), namely, through ordered motion. On the other hand, heat denotes the energy entering or leaving the system disorderly (window Q). Thus, by its very own construction, work has to be the same units as the energy of the system, even though they are different things.
