I only did the work less than a month ago so I am surprised that its already wearing down.
That's likely why.
Varnishes take time to complete the hardening process that converts them into their final cured form. This isn't just after they have dried. Broadly, it takes about a month1.
What this means is that after varnishing something ideally one should wait a full month after the last coat has been applied before putting it into service. Obviously in practice this isn't always feasible, but one should wait at minimum a couple of weeks. And until the requisite time has passed the item should be used lightly and with care.
After a full cure you won't be able to detect any smell from the finish with your nose right against the wood.
Any recommendations on what I should do
You need to refinish at least the affected areas. If you want to try to do a spot repair you need to dewax the entire area around the varnish losses using mineral spirits or paint thinner to start with.
Then I would recommend diluting some of your varnish in a fresh container (to convert it into 'wiping varnish', more on that here) and wiping on some light coats to the worn spots, aiming to blend them into the surrounding surfaces. You'll have to be the judge of whether these blend acceptably into the rest of the piece. If you find you can't do this to your liking you're looking at a complete refinish of the affected surfaces2.
Either way, of course wait a month before you lean against the desk much :-)
A note on wax
There is absolutely no need to wax freshly finished furniture.
You should ideally achieve whatever gloss level waxing gives you with the finish itself. Why use it in the first place otherwise?
By your own account you used the beeswax to polish up the piece, if you'd simply used a glossier varnish you'd have achieved the same end more directly, and far more durably — wax products, even the best of them with lots of harder waxes like carnauba in the formula, are merely furniture polishes and not finishes in their own right and they readily wear off surfaces (esp. arrises and corners) that see regular handling or rubbing.
1 That's for ideal conditions, it takes longer when the temperature is lower and/or the humidity is high.
2 In which case I highly recommend you don't sand again. Use a varnish stripper, this is what they're for.