After England lost the first Test against India in Ahmedabad on Monday, Broad hit out at ex-players, tweeting: "And before u listen to too many ex playing 'experts' being negative, ask them if they ever won a Test series in India... #28years."
That was perceived as being a response to the former England captain Botham, who had suggested Broad should be dropped for the second match of four which begins in Mumbai on Friday.
However he again took to Twitter to deny this.
"Spat with @BeefyBotham?? What spat? Love Beefy, best bowler England have ever had, then add his batting. Twitter is funny at times!" he tweeted.
Flower is conscious of the pitfalls of players' tweets - and although he does not consider Broad's latest remarks too significant a cause for regret, he has nonetheless spoken to him about them.
Flower said: "I don't think what he said was a big problem. Look, I've had a word with him about it already. You have to be very careful what you say on Twitter.
"With so many athletes using Twitter as often as they do and the journalists watching very closely what is said I think it's quite easy to write stories about some of the comments that are made.
"It's inevitable. We have to educate our players on doing it the right way. I think in the main our guys are pretty good. I don't think it [this episode] is a big thing."
Botham advocated Steven Finn's return to the side in Broad's place. That will not now be possible after Finn succumbed to a recurrence of a thigh strain for which he is to undergo a second scan on Wednesday.
England are expected to bring in a second spinner, however, with Tim Bresnan likely to make way for Monty Panesar - but Broad could also be dropped.