Sunshower, you beat me to answering this! *laughs* As Sunshower said, we're definitely aware of this, and here's what I tell everyone who writes in about this issue:
"We are aware of flowers being untouchable, and are working on this problem. You can water near them, and fertilize near them (if needed), which should keep them healthy. We do ask that you ignore these flowers for now, as we hope to resolve this within a future update."