When I first got it I transplanted it to a larger pot with bonsai soil. The pot has drainage. I was worried about it drying out so I started misting it in the morning (tell me it this is wrong).

This morning I found a small branch with cobweb like stuff on it and blackish leaves, I cut that branch off (again tell me if this was wrong).

Am I losing it?

Is it bad for a desk tree?

Pom are a semi tropical/ tropical plant inside at an office desk this time of year is wrong...... very wrong. Right would be a few more weeks outside at home full sun some shade. At the heated office desk would be okay during colder fall to winter and freezing temps.

Re-potting technically was wrong dont make it right by re-potting again wait if/when you re-pot again in a couple years or more aim for mid march to late march when your Pom is resting to help avoid re-potting shock effect

Pruning a Pom: Yes wrong again but the inside growing with AC office area could of been the reason for branch to web and blacken ( Mites ?) your cut wasn't wrong because.... Poms take well to pruning it induces growth and entices flowering. In Maine Poms back out side with daily and evening temps at 45-50... keep it protected inside at night during the late season frost times as well.

Watering Poms Odd as it is some need to stay moist at soil to damp some can handle drought, they all need watering at some time. I tend to agree with more water when growing less when not. Other questions you may have GW citrus and/ or tropical plants may be able to help you as well.