Jacob's phone symbol
For Jacob his phone symbolizes the security of his past life. It is useless in the loops of past but he keeps holding onto it and in times of crisis reaches for it in his pocket. The phone keeps him sane in a world full of insanity.
Hollows and wights as an allegory of human corruption
The monsters that keep hunting the peculiar children and their ymbryne were once human too. They've been corrupted with the hunger for power and they stop at nothing and do anything and everything to reach their goals. Their corruption is quite literally shown on the outside: hollows being empty monsters and wights having soulless white eyes. They lost everything that was human in them and are now a bizarre depiction of human corruption.
Miss Wren as a symbol of hope
Miss Wren as an actual person comes out only in the ending chapters. But the idea of her is present throughout the novel. She is a symbol of hope to the peculiar children; a last ymbryne that avoided captivity. She represents hope for the entire peculiar world and when she is captured as well it feels like that world is coming to an end.
Motif of landscape
Motif of landscape is connected to the theme of journey. The landscape changes when the peculiar children enter different loops. They get to see the same landscape from different time periods. In the menagerie loop there are no roads, the nature is wilder, in the 1940 London is in a time of war so there are destroyed buildings everywhere, sounds of sirens and bombs falling.
Symbolism of the St. Paul's cathedral
The history of St. Paul's cathedral is a symbol of human persistence. The cathedral was rebuilt throughout centuries despite always ending up destroyed. Of course, there is a peculiar influence to that persistence in the form of special pigeons.