Calculating Energy Consumption Using a Current Sensor and Voltage Sensor
I'm creating a PCBA that uses a hall-effect sensor to measure current
  and a transformer rectifier design to measure the mains voltage.


And


  But I seem to be getting errors in my Wh calculation


You don't measure power or watt hours that way. You are bound to get errors. Power is measured by multiplying the raw voltage AC waveform with the raw current AC waveform: -



Picture from here and here.

In order to avoid the effect of distorted current waveforms affecting the results you need to sample simultaneously both voltage and current waveforms AND at a high enough rate (typically 1 kSps for moderate accuracy).