Sorry, Shinji! She didn't mean anything by it. Nor does she realize that she's done something to sour his mood. So she's a tiny bit put off by his response, it seems... more curt than he's been so far.

"Oh, me either! I mean, I've planted some flowers I guess, but all I've ever really done is admire them!" She's still giving him a smile, trying to keep the air light. "But maybe if we work together - not just you and I, but all of us! - we can make this the best gardening experience ever!"

She's just... so optimistic, sorry Shinji.