Different colors are just for different numbers themselves. The game used to have all the numbers one color which you can still do in the options menu. The exception is yellow/turquoise/purple -- these colors signify an 'obscuring' enemy would have affected it had it not been revealed (usually showing a ?). When they are blended it means more than one enemy is affecting that specific tile. Yellow/Purple means there's a horizontal source and a radial source both affecting it.
90% of the enemies have a requirement for where they spawn. I'd say part of the fun of the game is learning these 'hidden' rules and using them to your advantage. There's some hints in the descriptions but some things are left to the user to discern. When you lose, take a peek at the board and try to reason some out. For example, a pair of Lovers are always facing each other on the same row.
