Stupidity: Given Enchantress' power, why not just try to cure Dr June Moone, so she can't threaten the world? That's what the government should've done.
Suggested correction: We're talking about Amanda Waller who had no issues murdering innocent government employees that were accidentally exposed to her top-secret Suicide Squad program they weren't cleared for (versus making them sign an NDA not to talk about it as in a real-life accidental exposure to uncleared employees). Waller just took the easier option which was to threaten to kill Enchantress if she didn't obey versus spending countless dollars (and exposing more people to Waller's program) trying to cure her.
Stupidity: Jake uses several Loops and travels all over the world in order to get back on the boat at the end of the film. This was completely unnecessary as only the final Loop in 1942, which was available to him in 2016, was the one he needed to enter despite the fact that its nature should have prevented him from reaching 1943 anyway.
Stupidity: During the movie, the bad guys keep the main character alive and free to roam the facility at will (even if they made him sign an incriminating form at the very beginning stating he's an inmate) doing absolutely nothing to restrict his freedom till the very end - he even retains personal effects like his broken Rolex and lighter, his wallet full of cash! He breaks into every forbidden area, picks up fights, damages property, escapes multiple times and 'corrupts' the person the whole facility is built for. He is worth absolutely nothing to them and has nobody waiting for him or that will look for him.