The consensus on the episode "The Pods" seems to be that the evil pod contained the piglets. I thought the same my first time watching, but upon rewatching I now think the second pod containing the magical wands could be the bad one. I haven't found anything else about this online, so if anyone has, please do link me :]

First of all the wands came out of the only thorned, "evil-looking" beanstalk.

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The 3 beanstalks

I'm sure most people suspected the second pod when it first sprouted from the ground. Secondly, I feel like it's pretty cliche to suspect the least suspicious person in law enforcement shows, but that may be my own personal thinking. Neither of these things, however, outweigh the fact that the piglets terrorize the town in the end of the episode. The reason I think they were good is after the wands drop from the pod Jake runs over to them and sprinkles glitter on them. 

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Jake sprinkling the piglets with (potentially evil) glitter.

It also appears that he sprinkles some on himself as well prior to that, but as he holds it over his head and he is 2-dimensional it's hard to tell if the glitter is falling on him or in front of him. The piglets could barely hold a pencil before that happened, and so I believe that adding glitter to them turned them evil, and they were nothing more than victims of the evil pod.