Noise issues Atmega power line
The decoupling capacitors for your Atmega should be directly across the supply pins and as close as possible to the pins. Try soldering a 100nF directly across pins 7 and 8 and also 20 and 22.

If you intend to relayout the PCB you need to think about getting the high current path off the groundplane and as short as possible. You have three sets of two outputs and three ground connects. Change the output ordering and group these as three sets of output-ground-output the ground is connected directly and only to the two transistors driving that output. You then add a single point connect from your groundplane to a point between the transistor sources to enable the gate drive. Use a separate logic ground connection.