samus usually has an okay time doing damage and a hard time dishing out kill moves. jigglypuff's low weight allows samus an easier time scoring kills.
samus has a strong projectile game while jigglypuff has none and is an air based character. usually to counter a projectile game, you stay on the ground. inherently, puff either has to use her strength against samus's strength, or sacrifice her air strength to have access to shielding the projectiles.
basically, when puff is not close, she is at a disadvantage.
at close range, puff does have a better grab than samus and her shorthop game allows her to have a few offensive options that samus does not. at this range, puff has to make sure not to get hit by up B (or DI out and punish, olol), try not to get pushed back to the midrange/longrange basically. and finally puff has to not die when she is at high percentage up close (dtilt is a big one, but dsmash, fsmash, even bair can be deadly up close)
puff sort of has a hard time killing samus. puff's offstage game triumphs samus' but samus has a tether that puff must be aware of in order to not miss out opportunities to gimp. samus also has bombs to control her aerial momentum, but of course jiggs has jumps.
this is all sort of basic on the surface stuff though, i'm not well versed enough in the game to go further.