Trivia: This episode first mentions the Breen species.
Data tells Timothy, "Androids do not lie." Yet in "Clues" he did just that the entire episode. Regardless of what deal he made with the Paxen aliens there, he still was lying in order to protect the Enterprise. And we don't even need to count how many times Lore lied; that's all he ever did.
When Timothy is building the temple when Data is present, watch Data. When part of the temple collapses Data jumps, as if he has been spooked. There's no indication Data has ever been programmed with a startlement circuit, given his superhuman reflexes and all.
Data finds fault about the temple Timothy was building. But after he build up the temple very fast and Timothy enters the room again after saying good-bye, the temple is neither perfect nor aesthetic - it's aslope and unsteady.
Data refers to Geordi as "Lieutenant LaForge" even though he has been a lieutenant commander for about two and a half years at this point.
Gene Roddenberry passed away during the filming of this episode.