The "three times" at the end was left intentionally ambiguous by the author, but a bit of background knowledge can't hurt.
The "traditional" way to pray at a Shinto shrine is to bow three times, clap three times, then bow once more (though this varies by type of shrine, era, etc). This is abbreviated to two bows, two claps, one bow in almost every instance in recent years. Hence, it's possible the ghost may be saying something like "I'll help you/forgive your rudeness this time, but make sure to pay your respects properly (by bowing three times) next time".
This was my first thought, and doesn't contradict any of the panels. The two smaller ghosts bowed to the big one, and then they frantically try to signal to Miko. One is shaking its head and the other is bowing; "no bow". I'm reasonably confident that this is the intended interpretation, but nothing is definitive and there's still some leeway for speculation.
There is also a saying that literally translates to "even a saint will only keep his composure up to three times", i.e. even the kindest person will get angry if they are repeatedly treated rudely. By this interpretation, the ghost might be saying "I'll only help you three (more) times". This ties in with the fact that Miko says "please" three times during her wish, implying he'll be taking his payment (her soul or something) once the three times are up; she said she'd "do anything".
In fact, it's not even clear that he's saying "three times". There are a number of other synonyms; "dispersal", in the sense of ghosts being exorcised (he just caused the ghost to disperse), "welcome (to my shrine)", or even "adjournment". Either way it's unclear and left as an exercise for the reader.