The House
The house is a symbol of protection for the children, guarding them the same way Miss Peregrine herself does. In Jacob's time, it also represents the past and all the secrets his grandfather has concealed from him. The house means many things to these children, which is why it is so devastating when the loop does not reset and the house gets destroyed by bombs.
The Apple
Before their first kiss, Emma picks an apple and gives it to Jacob while still inside the loop. The next morning, back in his own time, Jacob notices that the apple has completely aged and shriveled up. This apple is a symbol for the peculiar children themselves, as it is subject to the same forces that would rapidly age a peculiar child from the loop who spent too much time in the present. It is a reminder of the fragility of time and the consequences that result from shifting and bending it.
The Cairnholm Man
Early on in his stay at Cairnholm, Jacob comes upon the preserved, ancient body that the people of Cairnholm found in the bog. This corpse is a strong symbol for the past, which, as Jacob soon learns, is always present in Cairnholm.
Birds
Birds are a recurring motif in this story, both through Jacob's father's fascination with birdwatching and through the ymbrynes themselves, who are bird shapeshifters. Birds are given enormous power in this novel, as Miss Peregrine says that all birds—not just ymbrynes—have the power to manipulate time.
The Cairn
The cairn stands at the literal border between past and present, guarding the loop and its children of the past from the prying eyes of the people of the present. The cairn is also where they discovered the body of the bog boy, another prominent entity from the past that has found a place in the present. Thus, the cairn represents the dual world that Jacob has found himself in while on Cairnholm island.
