Percentage buildings taking net numbers instead of gross number?

Not sure if maybe I was seeing this wrong, but it looks like the percentage increase buildings take the net number and then the percentage instead of the gross then the percentage.  My point if a city is netting -1 gildar but grosses something like 4 or 5, the percentage will look at the -1 and not the 4 or 5.  How can you ever increase and get out of the negative if it is only looking at the net instead of the gross?

I haven't seen anything about this also, and wanted to see if maybe I was just seeing it wrong, but it seems this is the case.