ABSTRACT The ratio between secondary and primary cosmic ray (CR) particles is the main source of information about CR propagation in the Galaxy. Primary CRs are thought to be accelerated mainly in supernova remnant shocks and then released in the interstellar medium. Here, they produce secondary particles by occasional collisions with interstellar matter. As a result, the ratio between the fluxes of secondary and primary particles carries information about the amount of matter CRs have encountered during their journey from their sources to the Earth. Recent measurements by AMS-02 revealed an unexpected behaviour of two main secondary-to-primary ratios, the Boron-to-Carbon ratio and the antiproton-to-proton ratio. In this work, we discuss how such anomalies may reflect the action of two phenomena that are usually overlooked, namely the fact that some fraction of secondary particles can be produced within the acceleration region, and the non-negligible probability that secondary particles encounter an accelerator (and are re-accelerated) during propagation. Both effects must be taken into account in order to correctly extract information about CR transport from secondary-to-primary ratios.