The only way to fix it is to sand it all down, and get it smooth, then put some primer on the patch. If there are any patches, you dont have to fix, hopefully, you did primer them. The patch will always show, if it isnt primered, even if it isnt raised up like yours are. Make sure, it shows smooth after you have sanded and primered, before putting any paint on it. Did you use a nail punch to get those nails down below the surface of the shiplap? If not, that needs to be done. Only a tiny amount of filler would have had to be put on there then, and a quick wipe with a damp towel, and it would all have been smooth and ready for primer.

Is it MDF? Power nailers tend to raise a little of the MDF that needs to be sanded down as well. In locations that will not have moisture you can use a dab of drywall compound or spackling. It sands down smooth very quickly.