In "The Fear", Jonathan Crane—the Scarecrow's true identity—is "helping" Commissioner Gordon and the Super Powers Teams (the episode was part of the The Super Powers Team: Galactic Guardians era) capturing his alter ego ala Hannibal Lecter prior to the events of Red Dragon. However, the Scarecrow was also a member of the Legion of Doom during Challenge of the Superfriends and hence the few times the Legion of Doom stayed captured, the Super Friends and the police should've learned his identity prior to the episode.
Now it's possible that Crane escaped before he could be unmasked or positively identified as Jonathan Crane. Jonathan Crane might have been never been previously charged, and so might not be in any police database, which is still in 1970s methods and technology.
How did Dr. Rebos' androids infiltrate the first space mission as astronauts? What happened to the original astronauts who were supposed to be on the flight? Did the android astronauts (or some other androids) kidnap them? Nothing was mentioned about them after the crash.
Dr. Rebos and his assistant Loco disguised themselves as reporters and their truck as a van for Bow Wow magazine, then drove to the Cape Courageous base. They meet Wonder Dog and take several pictures of him (so they can make an android...er, canoid duplicate of him). They then give him a award for being "Dog of the Year" with his name on it. There's just one problem: the only reason Wonder Dog was outside the base is that he forgot his Top Secret pass and wasn't allowed inside. How exactly did Dr. Rebos know in advance that this would happen and Wonder Dog would be available?
"The Baffles Puzzle". The villains Dabny and Darby set up four traps to capture/delay the Super Friends so they don't interfere at the ransom dropoff. How did they know that Superman would go to investigate the "balloon floating free in the rain" and be taken out by the kryptonite hidden in it? While they could reasonably assume that Aquaman would check out "under the sea off the coast of Spain", what if Batman and Robin (in the Bat Jet or Bat Copter) or Wonder Woman (in her invisible jet) had gone to check out the balloon? The kryptonite would have been useless! And there was no kryptonite at all in the other traps, so if Superman had investigated them he wouldn't have been hampered in the slightest.
"The Fantastic FRERPS". The G.R.E.P.S. company knows from previous experience that when their shipments are hijacked the drivers are given a receipt signed "Roy La Post". Why don't they tell the delivery personnel that if they receive such a receipt, they're to immediately call in that they've been robbed and try to catch the robbers? When it happened in an early scene, the people didn't even bother to look at the receipt to see who signed it!
"Too Hot To Handle". Why exactly did the vine start attacking the museum at the beginning of the episode? The heat by itself wouldn't cause it, and there was no indication that the Solar-Terrarians had anything to do with it.
While Aquaman is a badass the "This Looks Like a Job for Aquaman" trope makes sense, because his signature abilities aren't all that useful on land. My question is, why did the writers have Black Manta's power being that he owned a boat? Black Manta's signature abilities since the Silver Age have been that he shoots laser beams out of his eyes. That's an awesome power.