Yes that happens. The QIF file does not carry any definition of whether a category is an Income or an Expense category, hence it can be misinterpreted.
Once a category has been created it is not possible to change the type. You need to take an indirect approach to facilitate this. We need to create a new category of the correct type and move the transactions to this new category.
As with any restructure you should take a backup before you start, but it is especially import here because any mistake can really damage your data.
Firstly create a new category of the correct type, it must have a different name to the existing category but you can rename it later. After doing this open the category you wish to change the type of, you do this by going to the category window through the menu command Tools → Categories, select the category then right click and in the drop down select “Open in New Window”.
This displays a register window – but note this is a category register window not the account type registers you are used to working with. Select all transaction in this register, generally you can do this by selecting a transaction then using the keyboard shortcut CTRL-A (CMD-A on Mac)
Now right click on the transactions and Select Batch Change. Select to Change the Account (yes that is Account). The software will then display a window where you can scroll down and select the Category to move the transactions to.
After pressing the OK button the transactions will be moved.
The original category should now be empty and you should be able to delete this category, note that if there are any subcategories you need to change their parent before deleting it. You can also rename the the new category if desired.