Two different sized batteries off one panel

It's not the size that's the problem, it's the voltage.

A PWM charge controller works by connecting the solar panel directly to the battery.  When the charge controller determines that the battery voltage is too high, it disconnects.  Then the voltage drops, and it reconnects.

What will happen in your situation is the 24 volt charge controller will connect and pretty much stay connected until the battery is fully charged.  The 12 volt charge controller will connect and have a near infinite supply of power at 24 volts.  Most PWM controllers don't like that -- solar panels are current-limited to the short circuit current of the panel, and batteries aren't.  With a 24 volt battery now directly connected to a 12 volt battery, bad things will happen -- a very large amount of current will flow from the 24 volt batteries, through the 24 volt charge controller, through the 12 volt charge controller, and finally to the 12 volt batteries.  Somewhere along the line something is going to blow a fuse, break or catch fire.

In short, don't do it.