I use a solvent based filler like plastic wood. Water based paints/fillers/caulk will react to unfinished MDF which is what nail holes and seams effectively are. This prevents water based fillers from setting/curing correctly as the MDF holds onto the filler moisture. I have used solvent based paintable caulking to fill tiny holes as well but it does shrink over time, so for seam repair or larger holes, it will look good for a few years but can shrink and separate/divot leaving a future repair for you, so something to consider.