I don't think this is something IC2 can fix -- you're missing a mod providing the Buildcraft API. Though I would've expected Forestry to provide it. It might be faster to bug Sengir about it.
IC² has a "special" BC-API, which is only getting loaded, when BC is loaded.
Using that API like any other Mod would do, would have the Sideeffect, that IC² has to come in two diffrent Versions (one for BC2 and one for BC3). And btw, Forestry has the BC-API.
The Geogenerator/Watermill should have at least a try/catch around that Part, to prevent Worldcorruption.
Edit: New Error for Watercapsules any item except IC²-Watercells
Display Spoiler
2012-08-27 12:17:39 [SEVERE] A critical error has occurred.
java.lang.NoSuchFieldError: filled
at buildcraft.api.BuildCraftAPI.getLiquidForFilledItem(BuildCraftAPI.java:51)
at ic2.bcIntegration31x.common.TileEntityWaterGeneratorBc31x.gainFuelSub(TileEntityWaterGeneratorBc31x.java:21)
at ic2.common.TileEntityWaterGenerator.gainFuel(TileEntityWaterGenerator.java:69)
at ic2.common.TileEntityBaseGenerator.n_(TileEntityBaseGenerator.java:118)
at xd.n(World.java:1971)
at net.minecraft.client.Minecraft.k(Minecraft.java:1871)
at net.minecraft.client.Minecraft.x(Minecraft.java:825)
at net.minecraft.client.Minecraft.run(Minecraft.java:753)
at java.lang.Thread.run(Unknown Source)