Momentum-dependent two-particle correlations in heavy-ion collisions can be fully characterized by a principal component analysis (PCA). In particular, subleading PCA modes of azimuthal Fourier harmonics are expected to reveal new information about hydrodynamic flow fluctuations. However, we find that as currently measured, it can instead be dominated by fluctuations of particle number, which can be measured independently and therefore represent redundant information that serves as an unwanted background. Here we propose a redefinition of the PCA observables which is insensitive to multiplicity fluctuations and thus free of redundancies. The proposed observables isolate novel sources of flow fluctuations from two-particle correlations and can provide fresh insight into the properties of the initial stages of the system at small length scales.