The transaction in on my debit card and I am currently having to import a file from my bank since I still cannot get them to set up the direct connect.
I have credited the $3.19 back to the Computer: Apps category which should cause at least $3.19 of the original $6.38 to credited just like you suggested. That is the way I have always recorded refunds in other FM software. The most strange thing about it is that the "Category Report" shows the Computer: Apps account as having a net expense of $6.38 instead of $3.19 as shown in the categories.jpg above.
If you manually enter a transaction for 6.38 payment against :apps and then another manual transaction for 3.19 deposit against :apps in the same register what happens? This is the very basic and standard operation of MD.. The category report should be correct..
I think it might be an idea to see what the category has in it, i.e. your second screen shot.
Go back to your category listing and right click on the category and select to open in a new window, don't change anything in this view it can be very dangerous to do so. Look at the "categories" in fact they will be the Account that the transaction is in. I suspect there may be an added transaction somewhere.
I'm just a user and created a couple of sample transactions and they reported correctly when I viewed the categories. I rarely look at Categories because it will include ALL transactions regardless of date so it quickly becomes nothing but a curiosity.
Try running an Income and Expense report and just include that particular category and do so just for the date range you are interested in.
dwg also had a good suggestion, right clicking on a transaction displayed in the Category window (or on a Mac a two finger tap) and Open Window will display all the transactions that are in that category.
However, there is one thing unusual that MoneyDance does with categories, if you select a main category such as "Fees & Charges" that has subcategories it appears to have those charges appear in the last subcategory. For example, I have some transactions labeled "Fees & Charges" but they show up if I select the "Fees & Charges: Trades and Commissions" in the Category window even though I have no transactions with that specific label.