Getting really close and ftilting when they just ran into you with shield: Wavedash back, bomb away or grab.
Dash attacking or dsmashing someone's shield: You'll get rocked for doing this. If it become apparent the opponent can or will shield, wavedash, then either wait, do a spaced tilt (this isn't even safe in certain MUs, puff can dair oos Marth can tipper fair), grab, or if you're really close anyway, bomb.
Up-B oos when the opponent is spaced away from you: Just reposition or lightshield or something.
Shield grabbing immediately after someone lands with an aerial: Look, you can shield grab smash attacks like Fox's usmash for free, but most people aren't going to just sit there in shield unless you've conditioned them with a lot of Up-B OoS connecting, or rolling away. You grab when you know they will shield, or you know they will stay on the ground and not dodge it (or when they simply can't avoid it). While it can also cover roll away, you have to use it sparringly.
Mindless missile spam: If the opponent isn't like, Bowser are something, they should very much be able to get around this, though you can still totally do it vs good characters. The "mindless" part is saying, you can still do it vs top tiers, but pay attention to how they move, you don't want to keep doing this if they're running at you or close.
Not watching for offstage snipes bomb-jumping: If the opponent goes offstage to edgeguard you, you can drift away from your bombs when bomb jumping and still do the bomb jump if you come back in. Don't let them just hit you free.
Rolling: Okay this isn't unusable, and sometimes may be necessary or even the best option (very, very rarely) but Samus's roll sucks and you should go out of your way to make sure it almost never happens as part of your movement. Wavedash, and do so earlier than you would have chosen to roll.
Jumping: Samus is a ground character. Even if you get a low% grab, dthrow -> nair if you drift in against another floaty can potentially get them more damage after the nair hits. Only go into the air as part of a combo, when you know you can hit air to air, and when you can do so in a way that doesn't leave you open to get hit right after, or do so to reposition and not approach. Or nair OoS if their percent is decent.
Wasting charge shot: It's a powerful long-range kill option to be sure, but the further they are, the more time they have to react, and the less of an ability you have to follow up on any pressure it may create or positioning it may get you. The closer you are... Well, the more of an ability you have to land other moves. Remember that the threat of the charge shot is something the opponent should respect.
