Translating the Setge de Calanda article from Catalan to Spanish with Apertium, most references are added at the end of the paragraph instead of their corresponding positions. Note in the example below, how the paragraph in the translation has 6 references at the end, while the original has those distributed in different sentences through the paragraph:

This quick link provides an easy to reproduce example (based on this example page with the problematic references). Note how all the references are added at the end (and two of them are labelled as "[1]", which is reported as a sepaate issue: T248380).