I created a footprint in Pattern Editor that contains a circle on the Bottom Assembly Layer. When I place that footprint on the PCB, it transposes the circle from the Bottom Assembly Layer to the Top Assembly Layer and now the circle no longer shows up on the Bottom Assembly Layer where it belongs. The gerbers confirm this as well.

On closer inspection of my PCB I noticed that when applying "change side" function to a SOT23 NPN trans. that pins 1 and 2 are transposed. Big problem, this circuit will not operate properly and goes undetected by the verifications.

kamus509, I don't know if our two issues are related or not, so do you think it might be a good idea to have them in separate threads for those who are experiencing similar issues as these (for clarity on down the line)?

Changing side for component moves top to bottom and back, so if you draw circle in Bottom Assy and then place component to Bottom - the circle will be in Top Assy - this is not a bug. Same with pins: when component is in bottom and you see it from the top, all pins are mirrored. To see how it will look from the bottom use "View/Mirror".