A reader of mine had a problem with iBooks book colors being inverted. That is, the background turned black instead of white and the content was white instead of black. This only happened when he was reading in low light.
iBooks has an Auto-Night theme. (This is different than the Accessibility color change). Auto-Night in iBooks automatically inverts colors when you are reading in low light. Using your device’s ambient light sensors, the colors on your screen change when it is dark, making the screen black and the words white.
You can turn Auto-Night mode on or off in the iBooks app. Tap the Font button (AA) in the upper right corner of the ebook. You’ll find the control there.
You can test the ambient light sensor of your iPad by covering it up. The location of the sensor is not the same for all iPad models. For example, my iPad Air 2 has two sensors, one near each of the corners at the top of the screen. So if you were wondering just what those two holes are for in your iPad Air 2 case, now you know. Cover both of them to turn Auto-Night on while viewing an iBook. You can find the location of the ambient light sensor(s) for any model iPad in Apple’s Developer Guidelines for Case Design. Look for the item(s) labeled ALS in the diagrams.