Yes, sometimes. It really rubbed me wrong how Team Galactic attacked that lake. All those dead Magicarp. Then, imagine how that will affect the ecosystem of that area. The pokemon living there will have to go somewhere else to find fresh water (since they can't drink sea water.). Then, when all the dead Magicarp begin to rot, there will be a massive influx of carrion feeders, which, trickle down theory here, will fruit parasites and disease. Ecoterrorism. (Not to mention the stench will cause people to not want to room at the nearby lodge, causing the owners of the lodge to lose money.)
And let us not forget Team Rocket murdering that Marowak and taking its baby Cubone.
They're assholes, but they're not as bad as, say Silent Hill's Pyramid Head, who goes around torturing and raping things. Of course, one must note that Pokemon is primarily a children's franchise, so the villians must be somewhat child friendly.
~Nemmeh