Stupidity: Given Louise's character, it makes no sense at all for her to leave Thelma in charge of the money. She's known Thelma for years, and knows fully well how flaky Thelma is. And Louise is shown as a person who lives by "If you want something right, you've gotta do it yourself". She's responsible, perhaps even uptight, at that point in the movie. So it defies everything about her character that she would let Thelma guard the money - it smells like a device set up just to allow the money to be stolen.
Stupidity: The Foot Clan knows that April O'Neil is an ally of the Teenage Mutant Ninja Turtles. Since the Foot Clan hasn't been able to find the Teenage Mutant Ninja Turtles for where they live a easy solution would be for them to go to April and ask where are the Teenage Mutant Ninja Turtles. An explanation is never given in the movie for why the Foot Clan never use that easy solution.
Suggested correction: First of all, the Foot Clan at the beginning of the movie is disorganized. Secondly, upon Shredder's return, he plants a Foot soldier named Freddy into April's news crew in order to keep an eye on her and find out where the Turtles are. Then they change tactics when they discover there is still some of the mutagenic ooze around, which they then decide to use to create their own mutants to lure the Turtles out of hiding.