Joining the output of 2 different power regulators
Why tie the 3v3 together? This should be avoided unless you have a specific reason like wanting to run a failsafe configuration, in which case you'll want to use schottky diodes to prevent back current in the simple case, or a PMIC if you want to be more thorough. The easier thing to do is just use one. Look up the schematics for both Pi boards. They will both have a 3v3 regulator probably integrated in a PMIC, and you don't want the two to fight with each other.