The +5V on bottom board is powered from top board.
Current situation is, when the top board and bottom board are attached, the +5V dropped down to +3.6V. I have confirmed the +5V power plane is not shortcut to ground.
After all components connected with +5V power plane are removed, the +5V is still dropped to +3.6V.
If you said all components have been removed, disconnect the bottom PCB that causes trouble and using an ohm-meter measure resistance between +5V and 0V ..
There has to be “something” that causes this voltage drop, for example a solder or copper bridge ..
I guess contamination during manufacturing is one possibility but the most common cause I have come across is splashing of the tin during hot air leveling causing an almost invisible short.