Pretty sure the studio wanted some kind of on screen subtitles which revealed what the probe was communicating about but Nimoy fought against it.
*edit*
When the alien probe is approaching Earth at the beginning to look for the humpback whales, there were originally subtitles saying things like "Where are you? Can you hear us?" The studio wanted to keep them despite Leonard Nimoy's objections. However, in the first test screening, test audiences indicated the subtitles were unnecessary, so they were cut.
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