Pilsner for instance tends to have a lot of DMS in it and the 90 minute boil time allows you to boil off all of the DMS. Other reasons might be the brewer wanted the hops to boil longer to get more IBU's so they planned for a longer boil. Continuous hopping techniques might require longer boil times to add all of the hops required in the recipe. You may need to boil off volume to hit your post boil volume targets. I'm sure there are other reasons but those are some of the ones I am aware of.