If you are using banking downloads, that is most likely the issue, they are being imported wrong. To find out you need to open a banking download in excel or something and look at entries for expense and income, one will be positive and the other negative for that type of entry.
I do not use banking downloads because of problems like this, so you will have to determine whether income is posting as a positive or negative. Most likely positive so all expenses should show as a negative number
in products and services, if you have plus and have marked the item as being both purchased and sold, edit the item and insure that the purchase side has an expense account selected and the sales side has an income account selected.
IF, if you do not have plus with that two sided feature - you can NOT use an item set up for expense on an invoice or sales receipt. Doing so will not increase income but will lower expense which serves to increase net income