It's a situation you generally want to avoid, yes. It's curious that they're not replacing Johansson's score, but are rather supplementing it and reworking it (with Johansson still involved, apparently). That's kind of an odd move. Even so, plenty of great movies have had scores replaced (or reworked), so it's not a sure-fire sign of major trouble with the film.
And honestly, I wasn't sold on Johansson as being a great fit for this movie in the first place. I'm like the one person who found his ARRIVAL score to be a big ol' bag of nothing.