What were the ACs, saves, and DCs of the relevant parties? CR is descriptive, not proscriptive, and if your level 4 players have a very good chance of either making their attack rolls or roflstomping the CR 8 / 9 enemy's saves then CR is unreliable.

Next time, more communication on the villains' part. Sending isn't a pocket change spell at those levels, but signal whistles are cheap.