After I had made a pure daisy and planted it. I surrounded it with stone. After the process of creating livingrock was done i destroyed all the livingrock blocks and the pure daisy with a vajra(Gravitation Suite mod) that had silktouch mode turned on(I was right clicking with it). When I right clicked on the pure daisy it dropped 2 pure daisys instead of 1.

Further testing showed that the same thing occurred with nightshade, daybloom, manastar, endoflame, spectrolus, kekimurus, entropinnym, munchdew and rosa arcana.
There can possibly be more flowers that this works for, but I have only tested with these.

FML Log: http://puu.sh/k4bD6/b28fa8f82f.log

Does something similar happen to things like grass or poppies?

Nope, it doesn't occur with grass or any vanilla minecraft flower.
I can further add that this happened on FTB Infinity 1.8.2 with Botania updated to the lastest version.