Hammer Bro 1: Where do you want these supplies, your ultimate evilness?
Bowser: Mmmm, right there in the corner's good enough.
Hammer Bro 2: Hey chief! What the hell's in those crates, anyway?
Hammer Bro 1: Yeah, you're taking rather heavy luggage for a simple time-travel trip.
Bowser: They're my pornographic magazines! What did you think they were?! Ummmm... I mean, they're the secret plans for the HYPER-DEATH RAY I plan to build one day.
That episode was very badly-written IMO. For one thing, how could Toad's periscope somehow pick up audio as well as visuals? How did it end up on the Doomship if Toad left it in Bowser's throne room? Why didn't Mario, Luigi, and Toad just smuggle themselves into separate crates? Why is it that Mario, Luigi, Toad, Bowser, and Ludwig could still talk normally when they were turned into babies? Why didn't the lady see anything strange about talking babies? Why did she think Bowser and Ludwig were the plumbers she called? Shouldn't she have been expecting the Marios? Where were the Mario Bros. of the past, anyway? Why didn't they appear anywhere in the past depicted? And how did Toad somehow change back to normal simply by jumping in the Doomship's window?
But I blame all those goofs on the fact that it was written by Rowby Goren, who had earlier written the first season episode "Mario's Magic Carpet", which was also badly-written and full of plot holes. By comparison, the episode "Toddler Terrors" aired with, "Reign Storm", was less stupid, but was still dumb. Why didn't Mario or Luigi notice anything strange about the Robot Peach? Why were the Mushroom People blaming the recent accidents on the two guys who had saved their lives so many times? And does anyone else think Cutter really did blab to other people that he'd been hanging out with a Princess from a video game? And furthermore, why did all the Mario characters refer to Earth as "the Real World"? Did they know that they didn't actually exist?
Simply put, the Mario cartoons were not well-written.