As seen in Alternate Character Interpretation. Most of the villains on the show are people who have spectacularly overreacted to some slight or setback in their life and decide to take it out on everyone else. With their natural abilities, personal wealth, and petty behaviour, the Spies themselves wouldnt be out of place in their own Rogues Gallery. Working for WOOHP helps prevent them from Jumping Off the Slippery Slope.
That said, the Series Fauxnale suggests that Evil is a genetic trait in this world.
Supporting the above, most every episode opens with the girls being faced with some high school drama they take very seriously, and what always happens immediately after? They get sucked away to Jerrys office.
It sounds strange that Geraldine Husk became obsessed with Clover, especially since it was Sam who exposed her organization as a hoax. But it makes sense when you keep Clover's character in mind — she's crazy for boys, she's a shopaholic, and she's the least focused of the spies.
Remember when Sam had to go undercover as Miss Spirit Fingers? There's a reason she wouldn't tell Alex or Clover about her mission; they, especially Alex, could not keep a secret. It's Character Development if I ever saw it.
Another example? In "Evil Valentine's Day", Sam gets suspicious when Jerry suddenly falls for former WOOHP agent (and future baddy) Myrna Beesbottom. After two episodes of falling in love with two villains ("Evil Boyfriend" and "Matchmaker" come to mind), she's clearly learned her lesson in that department.
At the end of "Astro-Not", Alex claims that she's been reading the wrong horoscope for herself the entire episode, before realizing she's actually a Pisces. Fittingly, back in "Aliens" Alex claims she's a Virgo. So that could mean Alex could have possibly been reading the Virgo horoscopes during the episode when in reality she was a Pisces.
The specific reason Jerry chose a cruise as the girls' test in "Deja Cruise". He mentions that the whole cruise would be a two week long affair. This was probably intentional, as it gives the girls a whole two weeks to figure out what was going on and pass the test. Not to mention, they could easily reset the cruise ship for the next day and the next test attempt and even have the girls wake up at the same time in the day.
Related to the above, the reason Alex's hair keeps going back to normal each day after the reset. Each day, the ship supposedly "sinks". We don't know exactly what happens, but if they do end up getting wet when the ship goes down, it would make sense why. Most perms or other hair curlings/alterations typically have the stipulation that they can't get wet for a certain amount of time, otherwise the bonds that shape the hair break and go back to normal. This usually a discouragement against taking a bath/shower or going swimming just after getting a perm. Very likely getting soaked in ocean water would absolutely revert one's hair in this case.
Just consider the countless schemes the villains in this show have: mutilation, destruction of property, terrorism, and murder. The spies may have fallen victim to them (albeit temporarily), but suppose they were brainwashed or mutilated permanently.
To make matters worse, imagine if one of them died. Ignoring Adult Fear, the remaining spies would have to create a cover story to explain such a loss.