Seems like the puzzles have levels

[Viper]

Based on the color of the tetranimo...Green easy...yellow intermediate...red difficult.

[ZIGS]

Not sure about that but I did just solve 2 red puzzles and they were the most difficult so far. Then again, could just be due to the natural progression of the game/difficulty

[tahgtahv]

Nope, the colors are for different types of puzzles, (grey for the tower, green for tools, yellow for temple access). Red ones give you red dots, of which I have many but found no use for yet. I haven't really paid attention to difficulty compared to color, but it's possible I guess.

[Nali]

Roughly accurate, yeah. Green sigils are what unlock the biggest chunks of the game, so they don't want anyone getting stuck on those, whereas yellows only unlock items, and reds unlock even less still in terms of raw content.

[AchromaticSky]

Yellows may "only" unlock items, but all items but the last are prerequisites for green sets, so they'll stop you from progressing just as quickly as greens. Specifically, the connector and cube are both required to access the second temple, and the fan and recorder are both required to access the third.