Pour a 3ft by 4 inches deep.all looks good. Took side boards off the next day notice some honeycomd on the side in some places.

That is a common situation that can be avoided by tapping on the sides of the form with a hammer (right when concrete is placed) to consolidate and/or with better vibration of the initial concrete placement.
If the concrete is still new (say 3 or so days or less since placed) a wet mix of sand and cement mortar (no larger aggegrate added) can be applied and worked into the voids.
If the honeycombed edge will be backfilled and not exposed, leaving it 'as is" is a fairly good option too.