If you have billable expense income in company settings set to an income account
and if you have checked the item as billable with a customer name when you enter the bill or expense payment
then that should do it
The only time I have seen odd entries in this area is when someone uses a journal entry - do you have any journal entries?
If so they need to be deleted and the bill or payment entered the way QBO was designed to work.
Journal entries should be the exception when using QB, they often do not work as you think they should, and when you use inventory type items they never work for inventory. It is much better to use the forms on the home page the way QB is designed to be used. Journal entries also bypass accrual/cash reporting, and will not show on many reports.