The easily accessible experimental signatures of Majorana modes are ambiguous and only probe topology indirectly: for example, quasi-Majorana states mimic most properties of Majoranas. Establishing a correspondence between an experiment and a theoretical model known to be topological resolves this ambiguity. Here we demonstrate that, already theoretically, determining whether a finite system is topological is by itself ambiguous. In particular, we show that the scattering topological invariant –a probe of topology most closely related to transport signatures of Majoranas–has multiple biases in finite systems. For example, we identify that quasi-Majorana states also mimic the scattering invariant of Majorana zero modes in intermediate-sized systems. We expect that the bias due to finite size effects is universal, and advocate that the analysis of topology in finite systems should be accompanied by a comparison with the thermodynamic limit. Our results are directly relevant to the applications of the topological gap protocol.