Anti-phase boundaries (APBs) are structural defects which have been shown to be responsible for the anomalous magnetic behavior observed in different nanostructures. Understanding their properties is crucial in order to use them to tune the properties of magnetic materials by growing APBs in a controlled way since their density strongly depends on the synthesis method. In this work we investigate their influence on magnetite (Fe3O4) thin films by considering an atomistic spin model, focussing our study on the role that the exchange interactions play across the APB interface. We conclude that the main atypical features reported experimentally in this material are well described by the model we propose here, confirming the new exchange interactions created in the APB as the responsible for this deviation from bulk properties.