At the risk of sound really stupid I need to ask how you breed the plants? Where do you go? 
Do the plants you breed have to be the exact same species too?
Sorry if this was already addressed. 
Plant breeding?
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Yes, they do need to be the same species. If you click a plant to view it, you'll see two sets of items on the left side: "Parents" and "Actions". Next two Actions, you'll see either three or four options. If the plant is breedable (that is, if there's a potential mate for it on your scroll, AND it's not an event plant that is only breedable for a specific time), then the first option on the list will be "breed". When you click that option, it will show you a list of available mates.
So, if you don't see the "breed" option, you need more of that plant. Occasionally a plant may need a different breed of plants for breeding; Lucky Clovers can only be mated with White Clovers, for instance, and can be bred all year round, it's just that if you breed them out of event time, all you'll get are White Clovers, not Lucky Clovers.
If there are particular plants you're curious about, it's best to be specific. Different plants have different requirements. St. Patty's Treasure can't be bred at all, for instance, although I think it might be the only plant with that limitation.
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On any adult plants page that is eligible to breed there will be an option that says breed on the same line as the other options (gift, trash, abandon). That will bring up a list of the available mates for that plant. Some plants breed with certain others, like jack o lanterns with pumpkins at halloween. Some plants only breed at certain times of the year (see above example lol). Hope that helps
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If there are particular plants you're curious about, it's best to be specific. Different plants have different requirements. St. Patty's Treasure can't be bred at all, for instance, although I think it might be the only plant with that limitation.
Snappy Tree Stumps are also unbreedable.
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Ah..I see.
Thank you for the reply.
