I'm pretty new to KSP and to modding it. I've been setting up a whole whack of mods for the past 12 hours or so, trying to make sure that everything is compatible before I start anything. Anyhow, I'm not certain how to test this exactly but based on what you've said, it sounds like some of those resources from USI hadn't been added to Dang It's blacklist configuration file. My understanding is that anything on that list won't be used for leaks in DangIt/Entropy.
Anyhow, I can't test it as I'm nowhere near making colonies but if you wanted to test it out, I poured through the USI code and extracted all the resource names that weren't in the DangIt config that I thought should be. So, the config file is at ~/GameData/DangIt/PluginData/DangIt/BlackList.cfg. Add this somewhere in the file:
//USI
ignore = MEP-Computing
ignore = MEP-Environmental
ignore = MEP-Mining
ignore = MEP-Laboratory
ignore = MEP-Manufacturing
ignore = MEP-Refining
ignore = MetallicOre
ignore = Metals
ignore = Polymers
ignore = Karbonite
ignore = PatchKits
ignore = RepairKits
ignore = ReplacementParts
ignore = BasicMachinery
ignore = AdvMachinery
ignore = SpecMachinery
ignore = PlasticParts
ignore = Robotics
ignore = Computers
ignore = ModularParts
ignore = Machinery
ignore = DepletedFuel
Let me know if that helps