There is a sensor which compares the left and right side current for each light system. Eg. current in left brake light is compared to current in right brake light. Sometimes when replacing a bulb on one side only it may draw more or less current than it's pair on the other side and fool the sensor into thinking that a light is out. Another possibility is that the contacts to one of the bulbs is poor and causing that side to draw more current. A final but not too common problem is that the bulb sensor is bad.

Try to figure out which "pair" is causing the problem by removing them at the same time. This should help you figure out the cause.

Dan