This has been tested with the latest 3.22.x and still needs to be confirmed in newer versions of Koha!

In the patron account, there are 3 different options for paying a fine. 2 show the payment as positive in green, one as negative in red. To test:

1) Add manual fee of any type
2) Pay using the pay button next to the fine entry (individual)
==> Verify the payment is displayed in red as positive amount
3) Add manual fee of any type
4) Pay using the "Pay selected" button at the bottom
==> Verify the payment is displayed in green as a negative amount
5) Add manual fee of any type
6) Pay using the "Pay amount" button at the bottom
==> Verify the payment is displayed in green as a negative amount

Koha itself seems to deal with it somehow, as the sum at the bottom of the table over all payments and fees is always correct.

But the difference is also visible in accountlines and can create quite a mess for reporting. One way to work around it currently is using ABS() before calculating with the amounts.